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Tsukahara K, Chang X, Mentch F, Smith-Whitley K, Bhandari A, Norris C, Glessner JT, Hakonarson H. Identification of genetic variants associated with clinical features of sickle cell disease. Sci Rep 2024; 14:20070. [PMID: 39209956 PMCID: PMC11362596 DOI: 10.1038/s41598-024-70922-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Sickle cell disease (SCD) is an inherited blood disorder marked by homozygosity of hemoglobin S, which is a defective hemoglobin caused by a missense mutation in the β-globin gene. However, clinical phenotypes of SCD vary among patients. To investigate genetic variants associated with various clinical phenotypes of SCD, we genotyped DNA samples from 520 SCD subjects and used a genome-wide association study (GWAS) approach to identify genetic variants associated with phenotypic features of SCD. For HbF levels, the previously reported 2p16.1 locus (BCL11A) reached genome significance (rs1427407, P = 8.58 × 10-10) in our GWAS as expected. In addition, we found a new genome-wide significance locus at 15q14 (rs8182015, P = 2.07 × 10-8) near gene EMC7. GWAS of acute chest syndrome (ACS) detected a locus (rs79915189, P = 3.70 × 10-8) near gene IDH2 at 15q26.1. The SNP, rs79915189, is also an expression quantitative trait locus (eQTL) of IDH2 in multiple tissues. For vasoocclusive episode (VOE), GWAS detected multiple significant signals at 2p25.1 (rs62118798, P = 4.27 × 10-8), 15q26.1 (rs62020555, P = 2.04 × 10-9) and 15q26.3 (rs117797325, P = 4.63 × 10-8). Our findings provide novel insights into the genetic mechanisms of SCD suggesting that common genetic variants play an important role in the presentation of the clinical phenotypes of patients with SCD.
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Affiliation(s)
- Katharine Tsukahara
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Research Institute, Leonard Madlyn Abramson Research Center, Suite 1216E, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Research Institute, Leonard Madlyn Abramson Research Center, Suite 1216E, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Kim Smith-Whitley
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anita Bhandari
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cindy Norris
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Research Institute, Leonard Madlyn Abramson Research Center, Suite 1216E, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Research Institute, Leonard Madlyn Abramson Research Center, Suite 1216E, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
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Alsultan A. Targeting BCL11A through gene therapy in sickle cell disease: Will one size fit all or most? Pediatr Blood Cancer 2024; 71:e30934. [PMID: 38468364 DOI: 10.1002/pbc.30934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024]
Affiliation(s)
- Abdulrahman Alsultan
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Oncology Center, King Saud University Medical City, Riyadh, Saudi Arabia
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Gambari R, Waziri AD, Goonasekera H, Peprah E. Pharmacogenomics of Drugs Used in β-Thalassemia and Sickle-Cell Disease: From Basic Research to Clinical Applications. Int J Mol Sci 2024; 25:4263. [PMID: 38673849 PMCID: PMC11050010 DOI: 10.3390/ijms25084263] [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: 03/04/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
In this short review we have presented and discussed studies on pharmacogenomics (also termed pharmacogenetics) of the drugs employed in the treatment of β-thalassemia or Sickle-cell disease (SCD). This field of investigation is relevant, since it is expected to help clinicians select the appropriate drug and the correct dosage for each patient. We first discussed the search for DNA polymorphisms associated with a high expression of γ-globin genes and identified this using GWAS studies and CRISPR-based gene editing approaches. We then presented validated DNA polymorphisms associated with a high HbF production (including, but not limited to the HBG2 XmnI polymorphism and those related to the BCL11A, MYB, KLF-1, and LYAR genes). The expression of microRNAs involved in the regulation of γ-globin genes was also presented in the context of pharmacomiRNomics. Then, the pharmacogenomics of validated fetal hemoglobin inducers (hydroxyurea, butyrate and butyrate analogues, thalidomide, and sirolimus), of iron chelators, and of analgesics in the pain management of SCD patients were considered. Finally, we discuss current clinical trials, as well as international research networks focusing on clinical issues related to pharmacogenomics in hematological diseases.
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Affiliation(s)
- Roberto Gambari
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, Department of Life Sciences and Biotechnology, Ferrara University, 40124 Ferrara, Italy
| | - Aliyu Dahiru Waziri
- Department of Hematology and Blood Transfusion, Ahmadu Bello University Teaching Hospital Zaria, Kaduna 810001, Nigeria;
| | - Hemali Goonasekera
- Department of Anatomy, Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, Colombo P.O. Box 271, Sri Lanka;
| | - Emmanuel Peprah
- Implementing Sustainable Evidence-Based Interventions through Engagement (ISEE) Lab, Department of Global and Environmental Health, School of Global Public Health, New York University, New York, NY 10003, USA;
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Hayeck TJ, Li Y, Mosbruger TL, Bradfield JP, Gleason AG, Damianos G, Shaw GTW, Duke JL, Conlin LK, Turner TN, Fernández-Viña MA, Sarmady M, Monos DS. The Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection. Genome Biol Evol 2024; 16:evae009. [PMID: 38302106 PMCID: PMC10853003 DOI: 10.1093/gbe/evae009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/03/2024] Open
Abstract
Regions under balancing selection are characterized by dense polymorphisms and multiple persistent haplotypes, along with other sequence complexities. Successful identification of these patterns depends on both the statistical approach and the quality of sequencing. To address this challenge, at first, a new statistical method called LD-ABF was developed, employing efficient Bayesian techniques to effectively test for balancing selection. LD-ABF demonstrated the most robust detection of selection in a variety of simulation scenarios, compared against a range of existing tests/tools (Tajima's D, HKA, Dng, BetaScan, and BalLerMix). Furthermore, the impact of the quality of sequencing on detection of balancing selection was explored, as well, using: (i) SNP genotyping and exome data, (ii) targeted high-resolution HLA genotyping (IHIW), and (iii) whole-genome long-read sequencing data (Pangenome). In the analysis of SNP genotyping and exome data, we identified known targets and 38 new selection signatures in genes not previously linked to balancing selection. To further investigate the impact of sequencing quality on detection of balancing selection, a detailed investigation of the MHC was performed with high-resolution HLA typing data. Higher quality sequencing revealed the HLA-DQ genes consistently demonstrated strong selection signatures otherwise not observed from the sparser SNP array and exome data. The HLA-DQ selection signature was also replicated in the Pangenome samples using considerably less samples but, with high-quality long-read sequence data. The improved statistical method, coupled with higher quality sequencing, leads to more consistent identification of selection and enhanced localization of variants under selection, particularly in complex regions.
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Affiliation(s)
- Tristan J Hayeck
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yang Li
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy L Mosbruger
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Adam G Gleason
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - George Damianos
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Grace Tzun-Wen Shaw
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jamie L Duke
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri S Monos
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Sahu S, Poplawska M, Lim SH, Dutta D. CRISPR-based precision medicine for hematologic disorders: Advancements, challenges, and prospects. Life Sci 2023; 333:122165. [PMID: 37832631 DOI: 10.1016/j.lfs.2023.122165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023]
Abstract
The development of programmable nucleases to introduce defined alterations in genomic sequences has been a powerful tool for precision medicine. While several nucleases such as zinc-finger nucleases (ZFN), transcriptor activator-like effector nucleases (TALEN), and meganucleases have been explored, the advent of CRISPR/Cas9 technology has revolutionized the field of genome engineering. In addition to disease modeling, the CRISPR/Cas9 technology has contributed to safer and more effective treatment strategies for hematologic diseases and personalized T-cell-based therapies. Here we discuss the applications of the CRISPR technology in the treatment of hematologic diseases, their efficacy, and ongoing clinical trials. We examine the obstacles to their successful use and the approaches investigated to overcome these challenges. Finally, we provide our perspectives to improve this genome editing tool for targeted therapies.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Building 560, Room 32-04, Frederick, MD 21702, USA.
| | - Maria Poplawska
- Department of Medicine (Division of Hematology and Oncology), State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Seah H Lim
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA
| | - Dibyendu Dutta
- Department of Medicine (Division of Hematology and Oncology), State University of New York Upstate Medical University, 750 E Adams, Syracuse, NY 13210, USA.
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Alshabeeb MA, Alwadaani D, Al Qahtani FH, Abohelaika S, Alzahrani M, Al Zayed A, Al Saeed HH, Al Ajmi H, Alsomaie B, Rashid M, Daly AK. Impact of Genetic Variations on Thromboembolic Risk in Saudis with Sickle Cell Disease. Genes (Basel) 2023; 14:1919. [PMID: 37895268 PMCID: PMC10606407 DOI: 10.3390/genes14101919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Sickle cell disease (SCD) is a Mendelian disease characterized by multigenic phenotypes. Previous reports indicated a higher rate of thromboembolic events (TEEs) in SCD patients. A number of candidate polymorphisms in certain genes (e.g., FVL, PRT, and MTHFR) were previously reported as risk factors for TEEs in different clinical conditions. This study aimed to genotype these genes and other loci predicted to underlie TEEs in SCD patients. METHODOLOGY A multi-center genome-wide association study (GWAS) involving Saudi SCD adult patients with a history of TEEs (n = 65) and control patients without TEE history (n = 285) was performed. Genotyping used the 10× Affymetrix Axiom array, which includes 683,030 markers. Fisher's exact test was used to generate p-values of TEE associations with each single-nucleotide polymorphism (SNP). The haplotype analysis software tool version 1.05, designed by the University of Göttingen, Germany, was used to identify the common inherited haplotypes. RESULTS No association was identified between the targeted single-nucleotide polymorphism rs1801133 in MTHFR and TEEs in SCD (p = 0.79). The allele frequency of rs6025 in FVL and rs1799963 in PRT in our cohort was extremely low (<0.01); thus, both variants were excluded from the analysis as no meaningful comparison was possible. In contrast, the GWAS analysis showed novel genome-wide associations (p < 5 × 10-8) with seven signals; five of them were located on Chr 11 (rs35390334, rs331532, rs317777, rs147062602, and rs372091), one SNP on Chr 20 (rs139341092), and another on Chr 9 (rs76076035). The other 34 SNPs located on known genes were also detected at a signal threshold of p < 5 × 10-6. Seven of the identified variants are located in olfactory receptor family 51 genes (OR51B5, OR51V1, OR51A1P, and OR51E2), and five variants were related to family 52 genes (OR52A5, OR52K1, OR52K2, and OR52T1P). The previously reported association between rs5006884-A in OR51B5 and fetal hemoglobin (HbF) levels was confirmed in our study, which showed significantly lower levels of HbF (p = 0.002) and less allele frequency (p = 0.003) in the TEE cases than in the controls. The assessment of the haplotype inheritance pattern involved the top ten significant markers with no LD (rs353988334, rs317777, rs14788626882, rs49188823, rs139349992, rs76076035, rs73395847, rs1368823, rs8888834548, and rs1455957). A haplotype analysis revealed significant associations between two haplotypes (a risk, TT-AA-del-AA-ins-CT-TT-CC-CC-AA, and a reverse protective, CC-GG-ins-GG-del-TT-CC-TT-GG-GG) and TEEs in SCD (p = 0.024, OR = 6.16, CI = 1.34-28.24, and p = 0.019, OR = 0.33, CI = 0.13-0.85, respectively). CONCLUSIONS Seven markers showed novel genome-wide associations; two of them were exonic variants (rs317777 in OLFM5P and rs147062602 in OR51B5), and less significant associations (p < 5 × 10-6) were identified for 34 other variants in known genes with TEEs in SCD. Moreover, two 10-SNP common haplotypes were determined with contradictory effects. Further replication of these findings is needed.
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Affiliation(s)
- Mohammad A. Alshabeeb
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Deemah Alwadaani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Farjah H. Al Qahtani
- Hematology/Oncology Center, King Saud University Medical City (KSUMC), Riyadh 11411, Saudi Arabia;
| | - Salah Abohelaika
- Research Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia;
- Pharmacy Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia
| | - Mohsen Alzahrani
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- King Fahad Hospital, Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Abdullah Al Zayed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hussain H. Al Saeed
- Hematology Department, Qatif Central Hospital (QCH), Qatif 32654, Saudi Arabia; (A.A.Z.); (H.H.A.S.)
| | - Hala Al Ajmi
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Barrak Alsomaie
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11426, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
| | - Mamoon Rashid
- King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia (M.A.)
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
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Kirkham JK, Estepp JH, Weiss MJ, Rashkin SR. Genetic Variation and Sickle Cell Disease Severity: A Systematic Review and Meta-Analysis. JAMA Netw Open 2023; 6:e2337484. [PMID: 37851445 PMCID: PMC10585422 DOI: 10.1001/jamanetworkopen.2023.37484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Importance Sickle cell disease (SCD) is a monogenic disorder, yet clinical outcomes are influenced by additional genetic factors. Despite decades of research, the genetics of SCD remain poorly understood. Objective To assess all reported genetic modifiers of SCD, evaluate the design of associated studies, and provide guidelines for future analyses according to modern genetic study recommendations. Data Sources PubMed, Web of Science, and Scopus were searched through May 16, 2023, identifying 5290 publications. Study Selection At least 2 reviewers identified 571 original, peer-reviewed English-language publications reporting genetic modifiers of human SCD phenotypes, wherein the outcome was not treatment response, and the comparison was not between SCD subtypes or including healthy controls. Data Extraction and Synthesis Data relevant to all genetic modifiers of SCD were extracted, evaluated, and presented following STREGA and PRISMA guidelines. Weighted z score meta-analyses and pathway analyses were conducted. Main Outcomes and Measures Outcomes were aggregated into 25 categories, grouped as acute complications, chronic conditions, hematologic parameters or biomarkers, and general or mixed measures of SCD severity. Results The 571 included studies reported on 29 670 unique individuals (50% ≤ 18 years of age) from 43 countries. Of the 17 757 extracted results (4890 significant) in 1552 genes, 3675 results met the study criteria for meta-analysis: reported phenotype and genotype, association size and direction, variability measure, sample size, and statistical test. Only 173 results for 62 associations could be cross-study combined. The remaining associations could not be aggregated because they were only reported once or methods (eg, study design, reporting practice) and genotype or phenotype definitions were insufficiently harmonized. Gene variants regulating fetal hemoglobin and α-thalassemia (important markers for SCD severity) were frequently identified: 19 single-nucleotide variants in BCL11A, HBS1L-MYB, and HBG2 were significantly associated with fetal hemoglobin (absolute value of Z = 4.00 to 20.66; P = 8.63 × 10-95 to 6.19 × 10-5), and α-thalassemia deletions were significantly associated with increased hemoglobin level and reduced risk of albuminuria, abnormal transcranial Doppler velocity, and stroke (absolute value of Z = 3.43 to 5.16; P = 2.42 × 10-7 to 6.00 × 10-4). However, other associations remain unconfirmed. Pathway analyses of significant genes highlighted the importance of cellular adhesion, inflammation, oxidative and toxic stress, and blood vessel regulation in SCD (23 of the top 25 Gene Ontology pathways involve these processes) and suggested future research areas. Conclusions and Relevance The findings of this comprehensive systematic review and meta-analysis of all published genetic modifiers of SCD indicated that implementation of standardized phenotypes, statistical methods, and reporting practices should accelerate discovery and validation of genetic modifiers and development of clinically actionable genetic profiles.
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Affiliation(s)
- Justin K. Kirkham
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Jeremie H. Estepp
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, Tennessee
- Now with Agios Pharmaceuticals, Cambridge, Massachusetts
| | - Mitch J. Weiss
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara R. Rashkin
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
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Paschoudi K, Yannaki E, Psatha N. Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies. Int J Mol Sci 2023; 24:ijms24119527. [PMID: 37298481 DOI: 10.3390/ijms24119527] [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: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies.
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Affiliation(s)
- Kiriaki Paschoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
- Department of Hematology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Ginete C, Delgadinho M, Santos B, Pinto V, Silva C, Miranda A, Brito M. Are Genetic Modifiers the Answer to Different Responses to Hydroxyurea Treatment?-A Pharmacogenetic Study in Sickle Cell Anemia Angolan Children. Int J Mol Sci 2023; 24:ijms24108792. [PMID: 37240136 DOI: 10.3390/ijms24108792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Sickle cell anemia (SCA) is an inherited disease affecting the hemoglobin that is particularly common in sub-Saharan Africa. Although monogenic, phenotypes are markedly heterogeneous in terms of severity and life span. Hydroxyurea is still the most common treatment for these patients, and the response to treatment is highly variable and seems to be an inherited trait. Therefore, identifying the variants that might predict hydroxyurea response is important for identifying patients who will have a poorer or non-response to treatment, and the ones that are more prone to suffer from severe side effects. In the present pharmacogenetic study, we analyzed the exons of 77 genes described in the literature as potentially associated with hydroxyurea metabolism in Angolan children treated with hydroxyurea and evaluated the drug response considering fetal hemoglobin levels, other hematological and biochemical parameters, hemolysis, number of vaso-occlusive crises and hospitalizations. Thirty variants were identified in 18 of those genes as possibly associated with drug response, five of them in gene DCHS2. Other polymorphisms in this gene were also associated with hematological, biochemical and clinical parameters. Further research examining the maximum tolerated dose and fixed dose with a larger sample size is necessary to corroborate these findings.
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Affiliation(s)
- Catarina Ginete
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
| | - Mariana Delgadinho
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
| | - Brígida Santos
- Centro de Investigação em Saúde de Angola (CISA), Bengo, Angola
- Hospital Pediátrico David Bernardino (HPDB), Luanda, Angola
| | - Vera Pinto
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
- Centro de Estatística e Aplicações, Universidade de Lisboa (CEAUL), 1749-016 Lisbon, Portugal
| | - Carina Silva
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
- Centro de Estatística e Aplicações, Universidade de Lisboa (CEAUL), 1749-016 Lisbon, Portugal
| | - Armandina Miranda
- Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Brito
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096 Lisbon, Portugal
- Centro de Investigação em Saúde de Angola (CISA), Bengo, Angola
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10
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Leibovitch JN, Tambe AV, Cimpeanu E, Poplawska M, Jafri F, Dutta D, Lim SH. l-glutamine, crizanlizumab, voxelotor, and cell-based therapy for adult sickle cell disease: Hype or hope? Blood Rev 2022; 53:100925. [PMID: 34991920 DOI: 10.1016/j.blre.2021.100925] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
For more than two decades, hydroxyurea was the only therapeutic agent approved by the Food and Drug Administration (FDA) for sickle cell disease (SCD). Although curative allogeneic hematopoietic stem cell transplants (allo-HSCT) were also available, only very few patients underwent the procedure due to lack of matched-related donors. However, therapeutic options for SCD patients increased dramatically in the last few years. Three new agents, l-glutamine, crizanlizumab, and voxelotor, were approved by the FDA for use in SCD patients. The number of SCD patients who underwent allo-HSCT also increased as a result of advances in the prevention of graft failure and graft-versus-host disease from using mismatched donor HSC. More recently gene therapy was made available on clinical trials. The increased treatment options for SCD have led to a sense of optimism and excitement among many physicians that these new approaches would alter the clinical course and disease burden. Although these newer agents do provide hope to SCD patients, the hyped-up responses need to be evaluated in the context of reality. In this review, we will discuss and compare these new agents and cell-based therapy, evaluate their clinical and economic impacts, and examine their roles in reducing the disease burden.
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Affiliation(s)
- Jennifer N Leibovitch
- Division of Hematology and Oncology, Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY, United States of America
| | - Ajay V Tambe
- Division of Hematology and Oncology, Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY, United States of America
| | - Emanuela Cimpeanu
- Division of Hematology and Oncology, Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States of America
| | - Maria Poplawska
- Division of Hematology and Oncology, Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States of America
| | - Firas Jafri
- Division of Hematology and Oncology, Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States of America
| | - Dibyendu Dutta
- Division of Hematology and Oncology, Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY, United States of America; Division of Hematology and Oncology, Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States of America
| | - Seah H Lim
- Division of Hematology and Oncology, Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY, United States of America; Division of Hematology and Oncology, Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States of America.
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11
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Unique Polymorphisms at BCL11A, HBS1L-MYB and HBB Loci Associated with HbF in Kuwaiti Patients with Sickle Cell Disease. J Pers Med 2021; 11:jpm11060567. [PMID: 34204365 PMCID: PMC8234980 DOI: 10.3390/jpm11060567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 11/16/2022] Open
Abstract
Patients with sickle cell disease (SCD) in Kuwait have elevated HbF levels ranging from ~10-44%; however, the modulating factors are unclear. We investigated the association of single nucleotide polymorphisms (SNPs) at BCL11A, HBS1L-MYB and HBB with HbF levels in 237 Kuwaiti SCD patients, divided into 3 subgroups according to their HbF levels. Illumina Ampliseq custom DNA panel was used for genotyping and confirmed by arrayed primer extension or Sanger sequencing. In the BCL11A locus, the CC genotype of rs7606173 [χ2 = 16.5] and (GG) of rs10195871 [χ2 = 15.0] were associated with Hb-F1 and HbF-2 subgroups, unlike rs1427404-T [χ2 = 17.3], which showed the highest association across the three subgroups. HBS1L-MYB locus revealed 2 previously-described SNPs (rs66650371 [χ2 = 9.5] and rs35795442 [χ2 = 9.2]) and 2 previously-unreported SNPs, (rs13220662 [χ2 = 6.2] and rs1406811 [χ2 = 6.7]) that were associated with the HbF-3 subgroup, making this the key locus elevating HbF to the highest levels. HBB cluster variants were associated with lower levels of HbF (β = -1.1). We report four previously-unpublished variants showing significant association with HbF. Each of the three quantitative trait loci affects HbF levels differently; unique SNPs, especially in HBS1L-MYB, elevate HbF to the highest levels.
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12
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Cyrus C, Vatte C, Chathoth S, Sayed AA, Borgio JF, Alrubaish MA, Alfalah R, Alsaikhan J, Al Ali AK. Haemoglobin switching modulator SNPs rs5006884 is associated with increased HbA 2 in β-thalassaemia carriers. Arch Med Sci 2021; 17:1064-1074. [PMID: 34336034 PMCID: PMC8314410 DOI: 10.5114/aoms.2019.86705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Haemoglobin A2 (HbA2), the tetramer of α- and δ-globin chains, is used as a diagnostic biomarker for β-thalassaemia carriers. The HbA2 levels are regulated by the presence of HPFH, δ-thalassaemia, HbA1/2 gene triplication, and variants of KLF1, β-globin gene, and HbF regulating QTLs. Saudi Arabia has a high incidence of borderline HbA2 levels, thereby making it difficult to classify the haemoglobinopathies. This study aims to investigate the association of known HbF enhancer QTL gene SNPs with HbA2 levels. MATERIAL AND METHODS 14 Specific SNPs in BCL11A, HMIP, OR51B6, HBBP1, and HBG2 loci were genotyped in 164 Saudi β-thalassaemia carriers by TaqMan assay to validate their role as regulators of HbA2 levels. HbA2 levels were determined using the Variant II β-Thalassemia Short Program Recorder kit. The non-random association of these SNPs was tested using HaploView software. Protein interaction was assessed using 3D structure modelling for OR51B6 (rs5006884), comparative energy minimisation, and root-mean-square deviation (RMSD) prediction. RESULTS Elevated HbA2 levels were associated with SNPs in HBBP1, OR51B6, and TCT haplotype from HBG2 promoter region. The bioinformatics modelling and prediction revealed that the exonic rs5006884 had RMSD value deviations and significantly varied binding energy minimisation. α-globin variations were found in 57.92% of individuals but were not associated with elevated HbA2. CONCLUSIONS The haemoglobin switching modulators rs2071348, rs7482144, and rs5006884 are involved in regulation of HbA2 level with rs5006884 influencing the tetramer formation. Screening for haemoglobinopathies should take these SNPs into consideration, specifically in borderline HbA2 cases. Assiduous analysis of rs5006884 as HbA2 modulator for amelioration of disease severity is recommended.
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Affiliation(s)
- Cyril Cyrus
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Chittibabu Vatte
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shahanas Chathoth
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdul Azeez Sayed
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Rawan Alfalah
- King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Jana Alsaikhan
- King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Amein K. Al Ali
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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13
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Urio F, Nkya S, Rooks H, Mgaya JA, Masamu U, Zozimus Sangeda R, Mmbando BP, Brumat M, Mselle T, Menzel S, Luzzatto L, Makani J. F cell numbers are associated with an X-linked genetic polymorphism and correlate with haematological parameters in patients with sickle cell disease. Br J Haematol 2020; 191:888-896. [PMID: 33073380 DOI: 10.1111/bjh.17102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/11/2020] [Indexed: 01/18/2023]
Abstract
Patients with sickle cell disease (SCD) with high fetal haemoglobin (HbF) tend to have a lower incidence of complications and longer survival due to inhibition of deoxyhaemoglobin S (HbS) polymerisation by HbF. HbF-containing cells, namely F cells, are strongly influenced by genetic factors. We measured the percentage of F cells (Fcells%) in 222 patients with SCD to evaluate the association of (i) Fcells% with genetic HbF-modifier variants and (ii) Fcells% with haematological parameters. There was a different distribution of Fcells% in females compared to males. The association of the B-cell lymphoma/leukaemia 11A (BCL11A) locus with Fcells% (β = 8·238; P < 0·001) and with HbF% (β = 2·490; P < 0·001) was significant. All red cell parameters except for Hb and mean corpuscular Hb concentration levels in males and females were significantly different. The Fcells% was positively associated with mean cell Hb, mean cell volume and reticulocytes. To explain the significant gender difference in Fcells%, we tested for associations with single nucleotide polymorphisms on the X chromosomal region Xp22.2, where a genetic determinant of HbF had been previously hypothesised. We found in males a significant association with a SNP in FERM and PDZ domain-containing protein 4 (FRMPD4) and adjacent to male-specific lethal complex subunit 3 (MSL3). Thus, we have identified an X-linked locus that could account for a significant fraction of the Fcells% variation in patients with SCD.
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Affiliation(s)
- Florence Urio
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Siana Nkya
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biological Sciences, Dar es salaam University College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Helen Rooks
- Comprehensive Cancer Centre, Kings College London, London, UK
| | - Josephine A Mgaya
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Upendo Masamu
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Zozimus Sangeda
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bruno P Mmbando
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- National Institute for Medical Research, Tanga, Tanzania
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Ted Mselle
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Stephan Menzel
- Comprehensive Cancer Centre, Kings College London, London, UK
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Julie Makani
- Muhimbili Sickle Cell Programme, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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14
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Steinberg MH. Fetal Hemoglobin in Sickle Hemoglobinopathies: High HbF Genotypes and Phenotypes. J Clin Med 2020; 9:jcm9113782. [PMID: 33238542 PMCID: PMC7700170 DOI: 10.3390/jcm9113782] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/30/2022] Open
Abstract
Fetal hemoglobin (HbF) usually consists of 4 to 10% of total hemoglobin in adults of African descent with sickle cell anemia. Rarely, their HbF levels reach more than 30%. High HbF levels are sometimes a result of β-globin gene deletions or point mutations in the promoters of the HbF genes. Collectively, the phenotype caused by these mutations is called hereditary persistence of fetal hemoglobin, or HPFH. The pancellularity of HbF associated with these mutations inhibits sickle hemoglobin polymerization in most sickle erythrocytes so that these patients usually have inconsequential hemolysis and few, if any, vasoocclusive complications. Unusually high HbF can also be associated with variants of the major repressors of the HbF genes, BCL11A and MYB. Perhaps most often, we lack an explanation for very high HbF levels in sickle cell anemia.
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Affiliation(s)
- Martin H Steinberg
- Department of Medicine, Division of Hematology/Oncology, Center of Excellence for Sickle Cell Disease, Center for Regenerative Medicine, Genome Science Institute, Boston University School of Medicine and Boston Medical Center, 72 E. Concord St., Boston, MA 02118, USA
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15
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Mohammadi Z, Mohammadi R, Haghpanah S, Moghadam M, Pazhoomand R, Karimi M. Association of Exon 14 of the SOX6 Gene Sequence Variations with Response to Hydroxyurea Therapy in Patients Carrying Non Transfusion-Dependent Thalassemia. Hemoglobin 2020; 44:406-410. [PMID: 33164584 DOI: 10.1080/03630269.2020.1845722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hydroxyurea (HU) activates the γ-globin gene, resulting in increased Hb F synthesis. The SOX6 gene is a member of the Sox (Sry-type HMG box) family of transcription factors, characterized by minor groove binding domain. The DNA binding domain of this gene is encoded by exon 14. We assessed the relationship between response to HU and exon 14 of the SOX6 gene sequence variations in patients with non transfusion-dependent thalassemia (NTDT). One hundred NTDT patients from southern Iran underwent HU therapy randomly participated in this cross-sectional study between February 2013 and October 2014. Based on response to HU therapy, the patients were divided into two groups: good and poor responder. Sequence variations of exon 14 of the SOX6 gene was assayed by the Sanger sequencing technique. From all evaluated single nucleotide polymorphisms (SNPs) as above, we found no significant association between sequence variations of exon 14 of the SOX6 gene and response to HU therapy (p > 0.05). It seems that no SNPs in exon 14 of the SOX6 gene is associated with response to HU in NTDT patients, but more studies are needed for further evaluation.
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Affiliation(s)
- Zahra Mohammadi
- Department of Pediatric Hematology/Oncology, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Mohammadi
- Department of Medical Genetics, Shiraz Infertility Treatment, Shiraz, Iran
| | - Sezaneh Haghpanah
- Department of Pediatric Hematology/Oncology, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Moghadam
- Department of Pediatric Hematology/Oncology, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Pazhoomand
- Department of Medical Genetics, Shiraz Infertility Treatment, Shiraz, Iran
| | - Mehran Karimi
- Department of Pediatric Hematology/Oncology, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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16
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Potential causal role of l-glutamine in sickle cell disease painful crises: A Mendelian randomization analysis. Blood Cells Mol Dis 2020; 86:102504. [PMID: 32949984 DOI: 10.1016/j.bcmd.2020.102504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 01/12/2023]
Abstract
In a recent clinical trial, the metabolite l-glutamine was shown to reduce painful crises in sickle cell disease (SCD) patients. To support this observation and identify other metabolites implicated in SCD clinical heterogeneity, we profiled 129 metabolites in the plasma of 705 SCD patients. We tested correlations between metabolite levels and six SCD-related complications (painful crises, cholecystectomy, retinopathy, leg ulcer, priapism, aseptic necrosis) or estimated glomerular filtration rate (eGFR), and used Mendelian randomization (MR) to assess causality. We found a potential causal relationship between l-glutamine levels and painful crises (N = 1278, odds ratio (OR) [95% confidence interval] = 0.68 [0.52-0.89], P = 0.0048). In two smaller SCD cohorts (N = 299 and 406), the protective effect of l-glutamine was observed (OR = 0.82 [0.50-1.34]), although the MR result was not significant (P = 0.44). We identified 66 significant correlations between the levels of other metabolites and SCD-related complications or eGFR. We tested these correlations for causality using MR analyses and found no significant causal relationship. The baseline levels of quinolinic acid were associated with prospectively ascertained survival in SCD patients, and this effect was dependent on eGFR. Metabolomics provide a promising approach to prioritize small molecules that may serve as biomarkers or drug targets in SCD.
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17
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El-Ghamrawy M, Yassa ME, Tousson AMS, El-Hady MA, Mikhaeil E, Mohamed NB, Khorshied MM. Association between BCL11A, HSB1L-MYB, and XmnI γG-158 (C/T) gene polymorphism and hemoglobin F level in Egyptian sickle cell disease patients. Ann Hematol 2020; 99:2279-2288. [PMID: 32772141 DOI: 10.1007/s00277-020-04187-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/15/2020] [Indexed: 01/17/2023]
Abstract
Sickle cell disease (SCD) is a monogenic disease characterized by multisystem morbidity and highly variable clinical course. Inter-individual variability in hemoglobin F (HbF) levels is one of the main modifiers that account for the clinical heterogeneity in SCD. HbF levels are affected by, among other factors, single nucleotide polymorphisms (SNPs) at the BCL11A gene and the HBS1L-MYB intergenic region and Xmn1 gene. Our aim was to investigate HbF-enhancer haplotypes at these loci to obtain a first overview of the genetic situation of SCD patients in Egypt and its impact on the severity of the disease. The study included 100 SCD patients and 100 matched controls. Genotyping of BCL11A (rs1886868 C/T), HBS1L-MYB (rs9389268 A/G) and Xmn1 γG158 (rs7842144 C/T) SNPs showed no statistically significant difference between SCD patients and controls except for the hetero-mutant genotypes of BCL11A which was significantly higher in SCD patients compared with controls. Baseline HbF levels were significantly higher in those with co-inheritance of polymorphic genotypes of BCL11A + HSB1L-MYB and BCL11A + Xmn1. Steady-state HbF levels, used as an indicator of disease severity, were significantly higher in SCD-Sβ patients having the polymorphic genotypes of HSB1L-MYB. Fold change of HbF in both patient groups did not differ between those harboring the wild and the polymorphic genotypes of the studied SNPs. In conclusion, BCL11A, HSB1L, and Xmn1 genetic polymorphisms had no positive impact on baseline HbF levels solely but had if coexisted. Discovery of the molecular mechanisms controlling HbF production could provide a more effective strategy for HbF induction.
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Affiliation(s)
- Mona El-Ghamrawy
- Pediatric Department, Pediatric Hematology & BMT Unit, Kasr Al-Ainy School of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Marianne E Yassa
- Clinical and Chemical Pathology Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Angie M S Tousson
- Pediatric Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Marwa Abd El-Hady
- Pediatric Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Kasr Al-Ainy St, Cairo, 11562, Egypt
| | - Erini Mikhaeil
- Pediatric and Neonatology, Ministry of Health, Cairo, Egypt
| | - Nada B Mohamed
- Misr University for Science and Technology, 6th of October City, Egypt
| | - Mervat Mamdooh Khorshied
- Clinical and Chemical Pathology Department, KasrAl-Ainy Faculty of Medicine, Cairo University, Cairo, Egypt.
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18
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Genc A, Tastemir Korkmaz D, Bayram S, Rencuzogullari E. The Effect of Five Single Nucleotide Polymorphisms on Hb F Variation of β-Thalassemia Traits and Hematologically Normal Individuals in Southeast Turkey. Hemoglobin 2020; 44:231-239. [PMID: 32674697 DOI: 10.1080/03630269.2020.1787178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
β-Thalassemia (β-thal) is caused by deficiency of β-globin chain synthesis and leads to the accumulation of unstable globin chain production. This results in a higher Hb F level in order to neutralize the excess α chains. In addition, γ-globin gene expression, due to genetic factors after birth, leads to increased Hb F levels in adulthood [hereditary persistence of fetal hemoglobin (Hb) (HPFH)]. In this study, the relationship between β-thal trait and individuals with suspected HPFH and a control group was investigated in Adıyaman, Turkey. Single nucleotide polymorphism (SNP) analyses were performed in five different polymorphic regions using real-time polymerase chain reaction (qPCR) methods [rs4671393 (G>A), rs766432 (A>C), rs9402686 (G>A), rs28384513 (T>G), rs1609812 (A>G)]. No significant difference was found between the control and β-thal group in the codominant inheritance model in the rs1609812 (A>G) polymorphism region only, while all the other polymorphic regions were found to be statistically significant. It was found that different genotype models increased Hb F levels between 1.6- and 3.06-fold in four studied polymorphic regions [rs4671393 (G>A), rs766432 (A>C), rs9402686 (G>A), rs28384513 (T>G)]. All of the polymorphic regions increased the Hb F levels from 1.86- to 24.76-fold, except rs9402686 (G>A) and rs28384513 (T>G) over dominant and rs1609812 (A>G) codominant inheritance models. The AC and AA genotypes increased Hb F levels in the B-cell CLL/lymphoma 11 A haplotype studies. It was determined that both haplotypes 2 and 4 increased Hb F levels. As a result, SNPs strongly affect the Hb F levels in both healthy individuals and β-thal trait.
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Affiliation(s)
- Ahmet Genc
- Vocational School of Health Services, Adıyaman University, Adıyaman, Turkey
| | | | - Suleyman Bayram
- Department of Nursing, School of Health, Adıyaman University, Adıyaman, Turkey
| | - Eyyup Rencuzogullari
- Department of Biology, Faculty of Science and Letters, Adıyaman University, Adıyaman, Turkey
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19
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Sales RR, Belisário AR, Faria G, Mendes F, Luizon MR, Viana MB. Functional polymorphisms of BCL11A and HBS1L-MYB genes affect both fetal hemoglobin level and clinical outcomes in a cohort of children with sickle cell anemia. Ann Hematol 2020; 99:1453-1463. [PMID: 32447424 DOI: 10.1007/s00277-020-04079-2] [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: 12/11/2019] [Accepted: 05/04/2020] [Indexed: 01/28/2023]
Abstract
Fetal hemoglobin (HbF) ameliorates clinical severity of sickle cell anemia (SCA). The major loci regulating HbF levels are HBB cluster, BCL11A, and HMIP-2 (HBS1L-MYB). However, the impact of noncoding single-nucleotide polymorphisms (SNPs) in these loci on clinical outcomes and their functional role on regulating HbF levels should be better elucidated. Therefore, we performed comprehensive association analyses of 14 noncoding SNPs in five loci with HbF levels and with clinical outcomes in a cohort of 250 children with SCA from Southeastern Brazil, and further performed functional annotation of these SNPs. We found SNPs independently associated with HbF levels: rs4671393 in BCL11A (β-coefficient = 0.28), rs9399137 in HMIP-2A (β-coefficient = 0.16), and rs4895441 in HMIP-2B (β-coefficient = 0.15). Patients carrying minor (HbF-boosting) alleles for rs1427407, rs93979137, rs4895441, rs9402686, and rs9494145 showed reduced count of reticulocytes (p < 0.01), while those carrying the T allele of rs9494145 showed lower white blood cell count (p = 0.002). Carriers of the minor allele for rs9402686 showed higher peripheral saturation of oxygen (p = 0.002). Patients carrying minor alleles in BCL11A showed lower risk of transfusion incidence rate ratio (IRR ≥ 1.3; p < 0.0001). This effect was independent of HbF effect (p = 0.005). Carriers of minor alleles for rs9399137 and rs9402686 showed lower risk of acute chest syndrome (IRR > 1.3; p ≤ 0.01). Carriers of the reference allele for rs4671393 showed lower risk of infections (IRR = 1.16; p = 0.01). In conclusion, patients carrying HbF-boosting alleles of BCL11A and HMIP-2 were associated with milder clinical phenotypes. Higher HbF concentration may underlie this effect.
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Affiliation(s)
- Rahyssa Rodrigues Sales
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil. .,Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil. .,Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
| | - André Rolim Belisário
- Centro de Tecidos Biológicos de Minas Gerais, Fundação Hemominas, Lagoa Santa, Minas Gerais, 33400-000, Brazil
| | - Gabriela Faria
- Serviço de Pesquisa, Fundação Hemominas, Belo Horizonte, Minas Gerais, Brazil
| | - Fabiola Mendes
- Serviço de Pesquisa, Fundação Hemominas, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo Rizzatti Luizon
- Programa de Pós-Graduação em Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Marcos Borato Viana
- Faculdade de Medicina/NUPAD, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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20
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Fong C, Mendoza Y, Barreto G. Genetic variants in the G gamma-globin promoter modulate fetal hemoglobin expression in the Colombian population. Genet Mol Biol 2020; 43:e20190076. [PMID: 32325484 PMCID: PMC7210980 DOI: 10.1590/1678-4685-gmb-2019-0076] [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: 03/12/2019] [Accepted: 11/28/2019] [Indexed: 11/23/2022] Open
Abstract
Fetal hemoglobin (HbF) is a determining factor for the development of sickle cell anemia. High HbF levels lower the intensity of symptoms of this disease. HbF levels can vary in patients with sickle cell anemia and individuals without the disease. The purpose of this study was to identify the genetic variants in the G gamma-globin gene promoter that can modulate HbF expression in patients with sickle cell anemia and healthy individuals from Colombia. In total, 413 bp of the G gamma-globin gene promoter were sequenced in 60 patients with sickle cell anemia and 113 healthy individuals. The allelic and genotype frequencies of the identified variants were compared between individuals with low and high HbF for both patients and healthy individuals. In total, we identified 15 variants in both groups, only three of which were shared between patients and healthy individuals. In healthy individuals, sites -16 and -309 (rs112479156) exhibited differences in allele frequencies. The mutant allele of -16 lowered the production of HbF, whereas the mutant allele of -309 increased its production. These results reveal the presence of different mechanisms of HbF regulation between patients with sickle cell and healthy individuals.
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Affiliation(s)
- Cristian Fong
- GIOD Group, Faculty of Dentistry, Universidad Cooperativa de Colombia, Pasto, Nariño, Colombia
| | - Yesica Mendoza
- Human Molecular Genetics Group, Biology Department, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Guillermo Barreto
- Human Molecular Genetics Group, Biology Department, Universidad del Valle, Cali, Valle del Cauca, Colombia
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21
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Bi W, Li Y, Smeltzer MP, Gao G, Zhao S, Kang G. STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing. Biostatistics 2020; 21:33-49. [PMID: 30007308 PMCID: PMC8559722 DOI: 10.1093/biostatistics/kxy030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/16/2018] [Accepted: 06/02/2018] [Indexed: 11/13/2022] Open
Abstract
It has been well acknowledged that methods for secondary trait (ST) association analyses under a case-control design (ST$_{\text{CC}}$) should carefully consider the sampling process to avoid biased risk estimates. A similar situation also exists in the extreme phenotype sequencing (EPS) designs, which is to select subjects with extreme values of continuous primary phenotype for sequencing. EPS designs are commonly used in modern epidemiological and clinical studies such as the well-known National Heart, Lung, and Blood Institute Exome Sequencing Project. Although naïve generalized regression or ST$_{\text{CC}}$ method could be applied, their validity is questionable due to difference in statistical designs. Herein, we propose a general prospective likelihood framework to perform association testing for binary and continuous STs under EPS designs (STEPS), which can also incorporate covariates and interaction terms. We provide a computationally efficient and robust algorithm to obtain the maximum likelihood estimates. We also present two empirical mathematical formulas for power/sample size calculations to facilitate planning of binary/continuous STs association analyses under EPS designs. Extensive simulations and application to a genome-wide association study of benign ethnic neutropenia under an EPS design demonstrate the superiority of STEPS over all its alternatives above.
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Affiliation(s)
- Wenjian Bi
- Department of Biostatistics, St. Jude Children’s Research
Hospital, Memphis, TN 38105, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel
Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel
Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina,
Chapel Hill, NC 27599, USA
| | - Matthew P Smeltzer
- Division of Epidemiology, Biostatistics, and Environmental Health, School of
Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago,
Chicago, IL 60637, USA
| | - Shengli Zhao
- School of Statistics, Qufu Normal University, Qufu 273165, PR
China
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children’s Research
Hospital, Memphis, TN 38105, USA
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22
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Belisário AR, da Silva AAS, Silva CVM, de Souza LMG, Wakabayashi EA, Araújo SDA, Simoes-e-Silva AC. Sickle cell disease nephropathy: an update on risk factors and potential biomarkers in pediatric patients. Biomark Med 2019; 13:967-987. [DOI: 10.2217/bmm-2019-0105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
One of the major chronic complications of sickle cell disease (SCD) is sickle cell nephropathy. The aim of this review is to discuss the pathophysiology, natural history, clinical manifestations, risk factors, biomarkers and therapeutic approaches for sickle cell nephropathy, focusing on studies with pediatric patients. The earliest manifestation of renal disease is an increase in the glomerular filtration rate. A finding that may also be observed in early childhood is microalbuminuria. Nephrin, KIM-1, VGFs, chemokines and renin-angiotensin system molecules have emerged as potential early markers of renal dysfunction in SCD. In regards to a therapeutic approach, renin-angiotensin system inhibitors and angiotensin receptor blockers seem to be effective for the control of albuminuria in adults with SCD, although new studies in children are needed. The precise moment to begin renoprotection in SCD patients who should be treated remains to be determined.
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Affiliation(s)
- André R Belisário
- Centro de Tecidos Biológicos de Minas Gerais, Fundação Hemominas, Rua das Goiabeiras, 779, Lagoa Santa, Minas Gerais 33400-000, Brazil
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Ariadna AS da Silva
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Cristiane VM Silva
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Larissa MG de Souza
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Eduarda A Wakabayashi
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Stanley de A Araújo
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
| | - Ana C Simoes-e-Silva
- Laboratório Interdisciplinar de Investigação Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Av Prof. Alfredo Balena, 190, Belo Horizonte, Minas Gerais 30130-100, Brazil
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23
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Cruz PRS, Ananina G, Gil-da-Silva-Lopes VL, Simioni M, Menaa F, Bezerra MAC, Domingos IF, Araújo AS, Pellegrino R, Hakonarson H, Costa FF, de Melo MB. Genetic comparison of sickle cell anaemia cohorts from Brazil and the United States reveals high levels of divergence. Sci Rep 2019; 9:10896. [PMID: 31350437 PMCID: PMC6659681 DOI: 10.1038/s41598-019-47313-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic analysis of admixed populations raises special concerns with regard to study design and data processing, particularly to avoid population stratification biases. The point mutation responsible for sickle cell anaemia codes for a variant hemoglobin, sickle hemoglobin or HbS, whose presence drives the pathophysiology of disease. Here we propose to explore ancestry and population structure in a genome-wide study with particular emphasis on chromosome 11 in two SCA admixed cohorts obtained from urban populations of Brazil (Pernambuco and São Paulo) and the United States (Pennsylvania). Ancestry inference showed different proportions of European, African and American backgrounds in the composition of our samples. Brazilians were more admixed, had a lower African background (43% vs. 78% on the genomic level and 44% vs. 76% on chromosome 11) and presented a signature of positive selection and Iberian introgression in the HbS region, driving a high differentiation of this locus between the two cohorts. The genetic structures of the SCA cohorts from Brazil and US differ considerably on the genome-wide, chromosome 11 and HbS mutation locus levels.
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Affiliation(s)
- Pedro R S Cruz
- Laboratory of Human Genetics, Centre for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Galina Ananina
- Laboratory of Human Genetics, Centre for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Vera Lucia Gil-da-Silva-Lopes
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Milena Simioni
- Department of Medical Genetics and Genomic Medicine, Faculty of Medical Sciences, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Farid Menaa
- Laboratory of Human Genetics, Centre for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Marcos A C Bezerra
- Genetics Postgraduate Program, Federal University of Pernambuco, Recife, PE, Brazil
| | - Igor F Domingos
- Genetics Postgraduate Program, Federal University of Pernambuco, Recife, PE, Brazil
| | - Aderson S Araújo
- Haematology and Haemotherapy Foundation of Pernambuco - HEMOPE, Recife, PE, Brazil
| | - Renata Pellegrino
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Fernando F Costa
- Haematology and Haemotherapy Centre, University of Campinas - UNICAMP, Campinas, São Paulo, Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Centre for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas - UNICAMP, Campinas, SP, Brazil.
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24
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Ferrucci V, de Antonellis P, Pennino FP, Asadzadeh F, Virgilio A, Montanaro D, Galeone A, Boffa I, Pisano I, Scognamiglio I, Navas L, Diana D, Pedone E, Gargiulo S, Gramanzini M, Brunetti A, Danielson L, Carotenuto M, Liguori L, Verrico A, Quaglietta L, Errico ME, Del Monaco V, D'Argenio V, Tirone F, Mastronuzzi A, Donofrio V, Giangaspero F, Picard D, Remke M, Garzia L, Daniels C, Delattre O, Swartling FJ, Weiss WA, Salvatore F, Fattorusso R, Chesler L, Taylor MD, Cinalli G, Zollo M. Metastatic group 3 medulloblastoma is driven by PRUNE1 targeting NME1-TGF-β-OTX2-SNAIL via PTEN inhibition. Brain 2019; 141:1300-1319. [PMID: 29490009 DOI: 10.1093/brain/awy039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/16/2018] [Indexed: 01/23/2023] Open
Abstract
Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-β signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-β activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common 'non-synonymous homozygous' deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-β/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3.10.1093/brain/awy039_video1awy039media15742053534001.
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Affiliation(s)
- Veronica Ferrucci
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy
| | - Pasqualino de Antonellis
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy.,Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada
| | - Francesco Paolo Pennino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Naples, Italy
| | | | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Naples, Italy
| | | | - Ida Pisano
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Luigi Navas
- Department of Veterinary Medicine and Animal Productions, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale della Ricerca, Naples, Italy
| | - Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale della Ricerca, Naples, Italy
| | - Sara Gargiulo
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale della Ricerca, Naples, Italy
| | - Matteo Gramanzini
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale della Ricerca, Naples, Italy
| | - Arturo Brunetti
- CEINGE Biotecnologie Avanzate, Naples, Italy.,Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Laura Danielson
- Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK
| | - Marianeve Carotenuto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Antonio Verrico
- Paediatric Neurosurgery, Ospedale Santobono-Pausilipon, Naples, Italy
| | - Lucia Quaglietta
- Paediatric Neurosurgery, Ospedale Santobono-Pausilipon, Naples, Italy
| | | | | | - Valeria D'Argenio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Felice Tirone
- Genetic Control of Development-URT, Institute of Cell Biology and Neurobiology, National Research Council, Fondazione Santa Lucia, Rome, Italy
| | - Angela Mastronuzzi
- Dipartimento di Onco-Ematologia, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | | | - Felice Giangaspero
- Dipartimento di Scienze Radiologiche, Oncologiche e Anatomo Patologiche, Università La Sapienza, Rome, Italy.,IRCCS Neuromed, Pozzilli, Italy
| | - Daniel Picard
- German Cancer Consortium (DKTK), Department of Paediatric Oncology, Haematology, and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Marc Remke
- German Cancer Consortium (DKTK), Department of Paediatric Oncology, Haematology, and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Livia Garzia
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, Canada
| | - Craig Daniels
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada
| | - Olivier Delattre
- PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Institut Curie, Paris, France
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Francesco Salvatore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Caserta, Italy
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London SM2 5NG, UK
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, Canada
| | - Giuseppe Cinalli
- Paediatric Neurosurgery, Ospedale Santobono-Pausilipon, Naples, Italy
| | - Massimo Zollo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy.,DAI-Medicina Trasfusionale-Azienda Ospedaliera Universitaria Federico II, Naples, Italy
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25
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Ilboudo Y, Bartolucci P, Garrett ME, Ashley-Koch A, Telen M, Brugnara C, Galactéros F, Lettre G. A common functional PIEZO1 deletion allele associates with red blood cell density in sickle cell disease patients. Am J Hematol 2018; 93:E362-E365. [PMID: 30105803 DOI: 10.1002/ajh.25245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/06/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Yann Ilboudo
- Faculty of Medicine; Université de Montréal; Montreal Quebec Canada
- Montreal Heart Institute; Montreal Quebec Canada
| | - Pablo Bartolucci
- Red Cell Genetic Disease Unit; Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP); Créteil France
| | - Melanie E. Garrett
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Allison Ashley-Koch
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Marilyn Telen
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Carlo Brugnara
- Department of Laboratory Medicine; Boston Children's Hospital; Boston Massachusetts
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit; Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP); Créteil France
| | - Guillaume Lettre
- Faculty of Medicine; Université de Montréal; Montreal Quebec Canada
- Montreal Heart Institute; Montreal Quebec Canada
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26
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Yahouédéhou SCMA, Adorno EV, da Guarda CC, Ndidi US, Carvalho SP, Santiago RP, Aleluia MM, de Oliveira RM, Gonçalves MDS. Hydroxyurea in the management of sickle cell disease: pharmacogenomics and enzymatic metabolism. THE PHARMACOGENOMICS JOURNAL 2018; 18:730-739. [DOI: 10.1038/s41397-018-0045-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 06/20/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023]
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27
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Mozeleski BM, Al-Rubaish A, Al-Ali A, Romero J. Perspective: A Novel Prognostic for Sickle Cell Disease. SAUDI JOURNAL OF MEDICINE & MEDICAL SCIENCES 2018; 6:133-136. [PMID: 30787839 PMCID: PMC6196691 DOI: 10.4103/sjmms.sjmms_107_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Sickle hemoglobin (α2βS 2) polymerization drives disease pathophysiology in sickle cell anemia. Fetal hemoglobin (α2γ2) restricts disease severity by inhibiting the polymerization of sickle hemoglobin in a concentration-dependent manner. Clinical decision-making relies on diagnostic technologies evaluating fetal hemoglobin as mean percent or mean quantity in blood. Limitation of this approach is exemplified by patients with significant high fetal hemoglobin levels and severe disease, suggesting that fetal hemoglobin is unevenly distributed across F-cells. Therefore, determination of fetal hemoglobin/F-cell would provide a new paradigm for ascertaining prognosis and response to fetal hemoglobin-inducing agents. Measurement of fetal hemoglobin/F-cell, ultimately adapted to widespread standardized analytical use, is a promising fetal hemoglobin-related prognostic approach to monitor the severity of sickle cell disease and the best "phenotype" to follow when developing new candidate fetal hemoglobin inducers or titrating hydroxyurea in treated sickle cell patients.
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Affiliation(s)
| | - Abdullah Al-Rubaish
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Amein Al-Ali
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
| | - Jose Romero
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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28
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Metformin induces FOXO3-dependent fetal hemoglobin production in human primary erythroid cells. Blood 2018; 132:321-333. [PMID: 29884740 DOI: 10.1182/blood-2017-11-814335] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/25/2018] [Indexed: 01/08/2023] Open
Abstract
Induction of red blood cell (RBC) fetal hemoglobin (HbF; α2γ2) ameliorates the pathophysiology of sickle cell disease (SCD) by reducing the concentration of sickle hemoglobin (HbS; α2βS2) to inhibit its polymerization. Hydroxyurea (HU), the only US Food and Drug Administration (FDA)-approved drug for SCD, acts in part by inducing HbF; however, it is not fully effective, reflecting the need for new therapies. Whole-exome sequence analysis of rare genetic variants in SCD patients identified FOXO3 as a candidate regulator of RBC HbF. We validated these genomic findings through loss- and gain-of-function studies in normal human CD34+ hematopoietic stem and progenitor cells induced to undergo erythroid differentiation. FOXO3 gene silencing reduced γ-globin RNA levels and HbF levels in erythroblasts, whereas overexpression of FOXO3 produced the opposite effect. Moreover, treatment of primary CD34+ cell-derived erythroid cultures with metformin, an FDA-approved drug known to enhance FOXO3 activity in nonerythroid cells, caused dose-related FOXO3-dependent increases in the percentage of HbF protein and the fraction of HbF-immunostaining cells (F cells). Combined HU and metformin treatment induced HbF additively and reversed the arrest in erythroid maturation caused by HU treatment alone. HbF induction by metformin in erythroid precursors was dependent on FOXO3 expression and did not alter expression of BCL11A, MYB, or KLF1. Collectively, our data implicate FOXO3 as a positive regulator of γ-globin expression and identify metformin as a potential therapeutic agent for SCD.
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29
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Bi W, Kang G, Pounds SB. Statistical selection of biological models for genome-wide association analyses. Methods 2018; 145:67-75. [PMID: 29803781 DOI: 10.1016/j.ymeth.2018.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/13/2018] [Accepted: 05/22/2018] [Indexed: 01/23/2023] Open
Abstract
Genome-wide association studies have discovered many biologically important associations of genes with phenotypes. Typically, genome-wide association analyses formally test the association of each genetic feature (SNP, CNV, etc) with the phenotype of interest and summarize the results with multiplicity-adjusted p-values. However, very small p-values only provide evidence against the null hypothesis of no association without indicating which biological model best explains the observed data. Correctly identifying a specific biological model may improve the scientific interpretation and can be used to more effectively select and design a follow-up validation study. Thus, statistical methodology to identify the correct biological model for a particular genotype-phenotype association can be very useful to investigators. Here, we propose a general statistical method to summarize how accurately each of five biological models (null, additive, dominant, recessive, co-dominant) represents the data observed for each variant in a GWAS study. We show that the new method stringently controls the false discovery rate and asymptotically selects the correct biological model. Simulations of two-stage discovery-validation studies show that the new method has these properties and that its validation power is similar to or exceeds that of simple methods that use the same statistical model for all SNPs. Example analyses of three data sets also highlight these advantages of the new method. An R package is freely available at www.stjuderesearch.org/site/depts/biostats/maew.
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Affiliation(s)
- Wenjian Bi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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30
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Biomarker signatures of sickle cell disease severity. Blood Cells Mol Dis 2018; 72:1-9. [PMID: 29778312 DOI: 10.1016/j.bcmd.2018.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
Identifying sickle cell disease patients at high risk of complications could lead to personalized treatment and better prognosis but despite many advances prediction of the clinical course of these patients remains elusive. We propose a system-type approach to discover profiles of multiple, common biomarkers that correlate with morbidity and mortality in sickle cell disease. We used cluster analysis to discover 17 signatures of 17 common circulating biomarkers in 2320 participants of the Cooperative Study of Sickle Cell Disease, and evaluated the association of these signatures with risk for stroke, pain, leg ulceration, acute chest syndrome, avascular necrosis, seizure, death, and trend of fetal hemoglobin and hemolysis using longitudinally collected data. The analysis shows that some of the signatures are associated with reduced risk for complications, while others are associated with increased risk for complications. We also show that these signatures repeat in two more contemporary studies of sickle cell disease and correlate with recently discovered biomarkers of pulmonary vascular disease. With replication and further study, these biomarker signatures could become an important and affordable precision medicine tool to aid treatment and management of the disease.
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31
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Raffield LM, Ulirsch JC, Naik RP, Lessard S, Handsaker RE, Jain D, Kang HM, Pankratz N, Auer PL, Bao EL, Smith JD, Lange LA, Lange EM, Li Y, Thornton TA, Young BA, Abecasis GR, Laurie CC, Nickerson DA, McCarroll SA, Correa A, Wilson JG, Lettre G, Sankaran VG, Reiner AP. Common α-globin variants modify hematologic and other clinical phenotypes in sickle cell trait and disease. PLoS Genet 2018; 14:e1007293. [PMID: 29590102 PMCID: PMC5891078 DOI: 10.1371/journal.pgen.1007293] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/09/2018] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
Co-inheritance of α-thalassemia has a significant protective effect on the severity of complications of sickle cell disease (SCD), including stroke. However, little information exists on the association and interactions for the common African ancestral α-thalassemia mutation (-α3.7 deletion) and β-globin traits (HbS trait [SCT] and HbC trait) on important clinical phenotypes such as red blood cell parameters, anemia, and chronic kidney disease (CKD). In a community-based cohort of 2,916 African Americans from the Jackson Heart Study, we confirmed the expected associations between SCT, HbC trait, and the -α3.7 deletion with lower mean corpuscular volume/mean corpuscular hemoglobin and higher red blood cell count and red cell distribution width. In addition to the recently recognized association of SCT with lower estimated glomerular filtration rate and glycated hemoglobin (HbA1c), we observed a novel association of the -α3.7 deletion with higher HbA1c levels. Co-inheritance of each additional copy of the -α3.7 deletion significantly lowered the risk of anemia and chronic kidney disease among individuals with SCT (P-interaction = 0.031 and 0.019, respectively). Furthermore, co-inheritance of a novel α-globin regulatory variant was associated with normalization of red cell parameters in individuals with the -α3.7 deletion and significantly negated the protective effect of α-thalassemia on stroke in 1,139 patients with sickle cell anemia from the Cooperative Study of Sickle Cell Disease (CSSCD) (P-interaction = 0.0049). Functional assays determined that rs11865131, located in the major alpha-globin enhancer MCS-R2, was the most likely causal variant. These findings suggest that common α- and β-globin variants interact to influence hematologic and clinical phenotypes in African Americans, with potential implications for risk-stratification and counseling of individuals with SCD and SCT.
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Affiliation(s)
- Laura M. Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jacob C. Ulirsch
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rakhi P. Naik
- Hematology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Samuel Lessard
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Robert E. Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Hyun M. Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nathan Pankratz
- Department of Laboratory Medicine & Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Erik L. Bao
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Ethan M. Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bessie A. Young
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Seattle Epidemiologic Research and Information Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Goncalo R. Abecasis
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Steven A. McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | | | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, Quebec, Canada
- Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (APR); (VGS)
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (APR); (VGS)
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32
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Chapin J, Giardina PJ. Thalassemia Syndromes. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00040-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Di J, Yang H, Jiang B, Wang Z, Ji J, Su X. Whole exome sequencing reveals intertumor heterogeneity and distinct genetic origins of sporadic synchronous colorectal cancer. Int J Cancer 2017; 142:927-939. [PMID: 29105743 DOI: 10.1002/ijc.31140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/26/2017] [Accepted: 10/16/2017] [Indexed: 12/24/2022]
Abstract
Sporadic synchronous colorectal cancer (CRC) refers to more than one primary tumor detected in a single patient at the time of the first diagnosis without predisposition of cancer development. Given the same genetic and microenvironment they raise, sporadic synchronous CRC is a unique model to study CRC tumorigenesis. We performed whole exome sequencing in 32 fresh frozen tumor lesions from 15 patients with sporadic synchronous CRC to compare their genetic alterations. This approach identified ubiquitously mutated genes in the range from 0.34% to 4.22% and from 0.8% to 7.0% in non-hypermutated tumors and hypermutated tumors, respectively, in a single patient. We show that both ubiquitously mutated genes and candidate cancer genes from different tumors in the same patient mutated at different sites. Consistently, obvious differences in somatic copy number variations (SCNV) were found in most patients with non-hypermutated tumor lesions, which had ubiquitous copy number amplification rates ranging from 0% to 8.8% and ubiquitous copy number deletion rates ranging from 0% to 8.2%. Hypermutated lesions were nearly diploid with 0% to 18.8% common copy number aberrations. Accordingly, clonal structures, altered signaling pathways and druggable genes in a single patient with synchronous CRC varied significantly. Taken together, the disparate SCNVs and mutations in synchronous CRC supported the field effect theory of tumorigenesis. Moreover, the intertumor heterogeneity of synchronous CRCs implies that analysis of all tumor lesions from the same patient is necessary for appropriate clinical treatment decisions.
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Affiliation(s)
- Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Hong Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Jiafu Ji
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biobank, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital and Institute, Beijing, People's Republic of China
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Habara AH, Shaikho EM, Steinberg MH. Fetal hemoglobin in sickle cell anemia: The Arab-Indian haplotype and new therapeutic agents. Am J Hematol 2017; 92:1233-1242. [PMID: 28736939 PMCID: PMC5647233 DOI: 10.1002/ajh.24872] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 12/28/2022]
Abstract
Fetal hemoglobin (HbF) has well-known tempering effects on the symptoms of sickle cell disease and its levels vary among patients with different haplotypes of the sickle hemoglobin gene. Compared with sickle cell anemia haplotypes found in patients of African descent, HbF levels in Saudi and Indian patients with the Arab-Indian (AI) haplotype exceed that in any other haplotype by nearly twofold. Genetic association studies have identified some loci associated with high HbF in the AI haplotype but these observations require functional confirmation. Saudi patients with the Benin haplotype have HbF levels almost twice as high as African patients with this haplotype but this difference is unexplained. Hydroxyurea is still the only FDA approved drug for HbF induction in sickle cell disease. While most patients treated with hydroxyurea have an increase in HbF and some clinical improvement, 10 to 20% of adults show little response to this agent. We review the genetic basis of HbF regulation focusing on sickle cell anemia in Saudi Arabia and discuss new drugs that can induce increased levels of HbF.
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Affiliation(s)
- Alawi H Habara
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, 02118
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Shaikho EM, Farrell JJ, Alsultan A, Qutub H, Al-Ali AK, Figueiredo MS, Chui DHK, Farrer LA, Murphy GJ, Mostoslavsky G, Sebastiani P, Steinberg MH. A phased SNP-based classification of sickle cell anemia HBB haplotypes. BMC Genomics 2017; 18:608. [PMID: 28800727 PMCID: PMC5553663 DOI: 10.1186/s12864-017-4013-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022] Open
Abstract
Background Sickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. As HbF is the major modulator of disease severity, classifying patients according to haplotype is useful. The first method of haplotype classification used restriction fragment length polymorphisms (RFLPs) to detect single nucleotide polymorphisms (SNPs) in the β-globin gene cluster. This is labor intensive, and error prone. Methods We used genome-wide SNP data imputed to the 1000 Genomes reference panel to obtain phased data distinguishing parental alleles. Results We successfully haplotyped 813 sickle cell anemia patients previously classified by RFLPs with a concordance >98%. Four SNPs (rs3834466, rs28440105, rs10128556, and rs968857) marking four different restriction enzyme sites unequivocally defined most haplotypes. We were able to assign a haplotype to 86% of samples that were either partially or misclassified using RFLPs. Conclusion Phased data using only four SNPs allowed unequivocal assignment of a haplotype that was not always possible using a larger number of RFLPs. Given the availability of genome-wide SNP data, our method is rapid and does not require high computational resources.
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Affiliation(s)
- Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - John J Farrell
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hatem Qutub
- Al-Omran Scientific Chair, King Faisal University, Al-Ahssa and Institute for Research & Medical Consultation, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Amein K Al-Ali
- Al-Omran Scientific Chair, King Faisal University, Al-Ahssa and Institute for Research & Medical Consultation, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | | | - David H K Chui
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Lindsay A Farrer
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - George J Murphy
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Gustavo Mostoslavsky
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, 72 E. Concord St, Boston, MA, 02118, USA.
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36
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Kuo KH. Multiple Testing in the Context of Gene Discovery in Sickle Cell Disease Using Genome-Wide Association Studies. GENOMICS INSIGHTS 2017; 10:1178631017721178. [PMID: 28811740 PMCID: PMC5542087 DOI: 10.1177/1178631017721178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/26/2017] [Indexed: 12/25/2022]
Abstract
The issue of multiple testing, also termed multiplicity, is ubiquitous in studies where multiple hypotheses are tested simultaneously. Genome-wide association study (GWAS), a type of genetic association study that has gained popularity in the past decade, is most susceptible to the issue of multiple testing. Different methodologies have been employed to address the issue of multiple testing in GWAS. The purpose of the review is to examine the methodologies employed in dealing with multiple testing in the context of gene discovery using GWAS in sickle cell disease complications.
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Affiliation(s)
- Kevin H.M. Kuo
- Departments of Medical Oncology and Hematology and Medicine, University Health Network, Toronto, ON, Canada
- Division of Hematology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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37
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Serjeant GR, Vichinsky E. Variability of homozygous sickle cell disease: The role of alpha and beta globin chain variation and other factors. Blood Cells Mol Dis 2017; 70:66-77. [PMID: 28689691 DOI: 10.1016/j.bcmd.2017.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/10/2017] [Accepted: 06/19/2017] [Indexed: 12/11/2022]
Abstract
The single base molecular substitution characterizing sickle cell haemoglobin, β6glu→val, might be expected to result in predictable haematological and clinical features. However, the disease manifests remarkable diversity believed to reflect the interaction with other genetic and environmental factors. Some of the genetic modifiers include the beta globin haplotypes, alpha thalassaemia, factors influencing the persistence of fetal haemoglobin and the effects of the environment are addressed in this review. It is concluded that much of the genetic data present conflicting results. Environmental factors such as climate and infections, and psychological, educational and social support mechanisms also influence expression of the disease. These interactions illustrate how the expression of a 'single gene' disorder may be influenced by a variety of other genetic and environmental factors.
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Affiliation(s)
- Graham R Serjeant
- Sickle Cell Trust (Jamaica), 14 Milverton Crescent, Kingston 6, Jamaica.
| | - Elliott Vichinsky
- Hematology/Oncology, UCSF Benioff Children's Hospital Oakland, University of California San Francisco, 747 52nd Street, Oakland, CA 94609, United States.
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38
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Ilboudo Y, Bartolucci P, Rivera A, Sedzro JC, Beaudoin M, Trudel M, Alper SL, Brugnara C, Galactéros F, Lettre G. Genome-wide association study of erythrocyte density in sickle cell disease patients. Blood Cells Mol Dis 2017; 65:60-65. [PMID: 28552477 DOI: 10.1016/j.bcmd.2017.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 12/14/2022]
Abstract
Deoxy-hemoglobin S polymerization into rigid fibers is the direct cause of the clinical sequelae observed in sickle cell disease (SCD). The rate of polymerization of sickle hemoglobin is determined primarily by intracellular hemoglobin concentration, itself dependent on the amount of sickle hemoglobin and on red blood cell (RBC) volume. Dense, dehydrated RBC (DRBC) are observed in SCD patients, and their number correlates with hemolytic parameters and complications such as renal dysfunction, leg ulcers and priapism. To identify new genes involved in RBC hydration in SCD, we performed the first genome-wide association study for DRBC in 374 sickle cell anemia (HbSS) patients. We did not find genome-wide significant results, indicating that variants that modulate DRBC have modest-to-weak effects. A secondary analysis demonstrated a nominal association (P=0.003) between DRBC in SCD patients and a variant associated with mean corpuscular hemoglobin concentration (MCHC) in non-anemic individuals. This intronic variant controls the expression of ATP2B4, the main calcium pump in erythrocytes. Our study highlights ATP2B4 as a promising target for modulation of RBC hydration in SCD patients.
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Affiliation(s)
- Yann Ilboudo
- Faculty of Medicine, Program in Bioinformatics, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Pablo Bartolucci
- Red Cell Genetic Disease Unit, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Est, IMRB - U955 - Equipe no 2, Créteil, France
| | - Alicia Rivera
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, USA; Department of Medicine, Harvard Medical School, Boston, USA
| | | | | | - Marie Trudel
- Faculty of Medicine, Department of Medicine and Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada; Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - Seth L Alper
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, USA; Department of Medicine, Harvard Medical School, Boston, USA
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Est, IMRB - U955 - Equipe no 2, Créteil, France
| | - Guillaume Lettre
- Faculty of Medicine, Program in Bioinformatics, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada.
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Chen Z, Zhao H, Fu N, Chen L. The diversified function and potential therapy of ectopic olfactory receptors in non-olfactory tissues. J Cell Physiol 2017; 233:2104-2115. [PMID: 28338216 DOI: 10.1002/jcp.25929] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 12/28/2022]
Abstract
Olfactory receptors (ORs) are mainly distributed in olfactory neurons and play a key role in detecting volatile odorants, eventually resulting in the production of smell perception. Recently, it is also reported that ORs are expressed in non-olfactory tissues including heart, lung, sperm, skin, and cancerous tissues. Interestingly, ectopic ORs are associated with the development of diseases in non-olfactory tissues. For instance, ectopic ORs initiate the hypoxic ventilatory responses and maintain the oxygen homeostasis of breathing in the carotid body when oxygen levels decline. Ectopic ORs induce glucose homeostasis in diabetes. Ectopic ORs regulate systemic blood pressure by increasing renin secretion and vasodilation. Ectopic ORs participate in the process of tumor cell proliferation, apoptosis, metastasis, and invasiveness. Ectopic ORs accelerate the occurrence of obesity, angiogenesis and wound-healing processes. Ectopic ORs affect fetal hemoglobin levels in sickle cell anemia and thalassemia. Finally, we also elaborate some ligands targeting for ORs. Obviously, the diversified function and related signal pathway of ectopic ORs may play a potential therapeutic target in non-olfactory tissues. Thus, this review focuses on the latest research results about the diversified function and therapeutic potential of ectopic ORs in non-olfactory tissues.
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Affiliation(s)
- Zhe Chen
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang, China
| | - Hong Zhao
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang, China
| | - Nian Fu
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, University of South China, Hengyang, China
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Relationship Between Some Single-nucleotide Polymorphism and Response to Hydroxyurea Therapy in Iranian Patients With β-Thalassemia Intermedia. J Pediatr Hematol Oncol 2017; 39:e171-e176. [PMID: 28121747 DOI: 10.1097/mph.0000000000000779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To evaluate the possible relationship between hydroxyurea (HU) response and some single-nucleotide polymorphism (SNP) in patients affected by β-thalassemia intermedia. MATERIALS AND METHODS In this cross-sectional study, 100 β-thalassemia intermedia patients who were taking HU with a dose of 8 to 15 mg/kg body weight per day for a period of at least 6 months were randomly selected between February 2013 and October 2014 in southern Iran. HU response was defined based on decrease or cessation of the blood transfusion need and evaluation of Hb level. RESULTS In univariate analysis, from all evaluated SNPs, only rs10837814 SNP of olfactory receptors (ORs) OR51B2 showed a significant association with HU response (P=0.038) and from laboratory characteristics, only nucleated red blood cells showed significant associations (116%±183%) in good responders versus (264%±286%) in poor responders (P=0.045). In multiple logistic regression, neither laboratory variables nor different SNPs, showed significant association with HU response. Three novel nucleotide variations (-665 [A→C], -1301 [T→G],-1199 delA) in OR51B2 gene were found in good responders. CONCLUSIONS None of the evaluated SNPs in our study showed significant association with HU response. Further larger studies and evaluation of other genes are suggested.
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Lai Y, Chen Y, Chen B, Zheng H, Yi S, Li G, Wei H, He S, Zheng C. Genetic Variants at BCL11A and HBS1L-MYB loci Influence Hb F Levels in Chinese Zhuang β-Thalassemia Intermedia Patients. Hemoglobin 2017; 40:405-410. [PMID: 28361591 DOI: 10.1080/03630269.2016.1253586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Increased Hb F levels can ameliorate the symptoms of β-thalassemia (β-thal). Due to the genetic heterogenicity of β-thal, the relationship between genetic variants in modifier genes and Hb F level has been studied in different populations. The Chinese Zhuang has the second largest population in China and has 6.78% prevalence of β-thal. However, the effects of these single nucleotide polymorphism (SNP) variants on the Hb F levels of β-thal intermedia (β-TI) patients in this population have not been reported. To explore the association between modifier loci (β-globin gene cluster, HBS1L-MYB intergenic region and BCL11A) and Hb F levels in Chinese Zhuang β-TI patients, 96 unrelated β-TI patients (50 males and 46 females) with different Hb F levels were recruited and genotyped by mass spectrometry. A total of 13 SNPs were confirmed to be in a significant relationship with Hb F levels in this population. Of these, high-risk genotypes of six Hb F-associated SNPs, rs9376090, rs7776054, rs9399137, rs9389268, rs9402685 in the HBS1L-MYB intergenic region and rs189984760 in the BCL11A locus, showed association with high Hb F levels, especially for SNPs in linkage disequilibrium. One novel Hb F-associated SNP, rs189984760, was identified in our study. Our findings will be of valuable reference for correlation between modifier genes and Hb F in Chinese Zhuang populations and may lead to better understand the modifying mechanisms for β-thal.
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Affiliation(s)
- Yunli Lai
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Yun Chen
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Biyan Chen
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Haiyang Zheng
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Sheng Yi
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Guojian Li
- b Guangxi Health and Family Planning Commission , Nanning , Guangxi Province , People's Republic of China
| | - Hongwei Wei
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Sheng He
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
| | - Chenguang Zheng
- a Genetic and Metabolic Central Laboratory , Guangxi Zhuang Autonomous Region Women and Children Care Hospital , Nanning , Guangxi Province , People's Republic of China
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Mikobi TM, Tshilobo Lukusa P, Aloni MN, Lumaka AZ, Kaba DK, Devriendt K, Matthijs G, Mbuyi Muamba JM, Race V. Protective BCL11A and HBS1L-MYB polymorphisms in a cohort of 102 Congolese patients suffering from sickle cell anemia. J Clin Lab Anal 2017; 32. [PMID: 28332727 DOI: 10.1002/jcla.22207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/21/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We aimed to investigate the distribution of selected BCL11A and HMIP polymorphisms (SNP's), and to assess the correlation with HPFH in a cohort of sickle cell patients. METHODS A preliminary cross-sectional study was conducted in 102 patients. Group 1 was composed of patients with HPFH and Group 2 consisted of patients without HbF. We assessed 8 SNPs previously associated with HPFH in cohorts genetically close to the Congolese population. Observed frequencies were compared to expected frequencies. RESULTS In the group 1, at rs7606173, the observed frequency for the genotype GG was significantly higher and the genotype GC was significantly lower than their respective expected frequencies. At rs9399137, the observed frequency of the genotype TT was significantly lower than expected. Conversely, the observed frequency of the genotype TC was significantly higher than expected. The observed frequency of the genotype TT at rs11886868 was significantly lower than the expected whereas the frequency of the genotype TC was significantly higher than observed. The lowest HbF level was recorded in patients with genotype CC at rs11886868. CONCLUSION In this preliminary study, the results demonstrate that alleles of some of the 8 studied SNPs are not randomly distributed among patients with or without HPFH in this cohort.
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Affiliation(s)
- Tite Minga Mikobi
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department des Sciences de Bases, Laboratory of Biochemistry and Molecular Biology, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Sickle Cell Center of Yolo, Kinshasa, Democratic Republic of Congo
| | - Prosper Tshilobo Lukusa
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Michel Ntetani Aloni
- Division of Hemato-oncology and Nephrology, Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Aimé Zola Lumaka
- Center for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo.,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.,Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Didine Kinkodi Kaba
- Division of Biostatistics and Epidemiology, School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Koenraad Devriendt
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Gert Matthijs
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jean Marie Mbuyi Muamba
- Division of Hemato-Immuno-Rheumatology, Department of Internal Medicine, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Valérie Race
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
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43
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Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet 2017; 49:625-634. [PMID: 28218758 PMCID: PMC5374001 DOI: 10.1038/ng.3793] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants from genome-wide association studies largely cluster in regulatory DNA. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating mutagenesis libraries with single or combinatorial nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, a locus associated with red blood cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false positive regions, which emphasizes the importance of off-target analysis in design of saturating mutagenesis experiments. Taken together, these data establish a widely applicable high-throughput and high-resolution methodology to reliably identify minimal functional sequences within large regions of disease- and trait-associated DNA.
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Affiliation(s)
- Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel Lessard
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Luca Pinello
- Department of Molecular Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Yann Ilboudo
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Emily N Stern
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Austen J Needleman
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit, Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), UPeC, IMRB U955 Equipe no. 2, Créteil, France
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Abdullah Kutlar
- Department of Medicine, Sickle Cell Center, Augusta University, Augusta, Georgia, USA
| | - Colin McKenzie
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Marvin Reid
- The Caribbean Institute for Health Research, University of the West Indies, Mona, Kingston, Jamaica
| | - Diane D Chen
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Partha Pratim Das
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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44
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Existence of HbF Enhancer Haplotypes at HBS1L-MYB Intergenic Region in Transfusion-Dependent Saudi β-Thalassemia Patients. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1972429. [PMID: 28280727 PMCID: PMC5322420 DOI: 10.1155/2017/1972429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/14/2016] [Accepted: 01/16/2017] [Indexed: 12/21/2022]
Abstract
Background and Objectives. β-Thalassemia and sickle cell disease are genetic disorders characterized by reduced and abnormal β-globin chain production, respectively. The elevation of fetal hemoglobin (HbF) can ameliorate the severity of these disorders. In sickle cell disease patients, the HbF level elevation is associated with three quantitative trait loci (QTLs), BCL11A, HBG2 promoter, and HBS1L-MYB intergenic region. This study elucidates the existence of the variants in these three QTLs to determine their association with HbF levels of transfusion-dependent Saudi β-thalassemia patients. Materials and Methods. A total of 174 transfusion-dependent β-thalassemia patients and 164 healthy controls from Eastern Province of Saudi Arabia were genotyped for fourteen single nucleotide polymorphisms (SNPs) from the three QTL regions using TaqMan assay on real-time PCR. Results. Genotype analysis revealed that six alleles of HBS1L-MYB QTL (rs9376090C p = 0.0009, rs9399137C p = 0.008, rs4895441G p = 0.004, rs9389269C p = 0.008, rs9402686A p = 0.008, and rs9494142C p = 0.002) were predominantly associated with β-thalassemia. In addition, haplotype analysis revealed that haplotypes of HBS1L-MYB (GCCGCAC p = 0.022) and HBG2 (GTT p = 0.009) were also predominantly associated with β-thalassemia. Furthermore, the HBS1L-MYB region also exhibited association with the high HbF cohort. Conclusion. The stimulation of HbF gene expression may provide alternative therapies for the amelioration of the disease severity of β-thalassemia.
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45
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Riaz M, Lorés-Motta L, Richardson AJ, Lu Y, Montgomery G, Omar A, Koenekoop RK, Chen J, Muether P, Altay L, Schick T, Fauser S, Smailhodzic D, van Asten F, de Jong EK, Hoyng CB, Burdon KP, MacGregor S, Guymer RH, den Hollander AI, Baird PN. GWAS study using DNA pooling strategy identifies association of variant rs4910623 in OR52B4 gene with anti-VEGF treatment response in age-related macular degeneration. Sci Rep 2016; 6:37924. [PMID: 27892514 PMCID: PMC5124940 DOI: 10.1038/srep37924] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/02/2016] [Indexed: 12/20/2022] Open
Abstract
Pooled DNA based GWAS to determine genetic association of SNPs with visual acuity (VA) outcome in anti-vascular endothelial growth factor (anti-VEGF) treated neovascular age-related macular degeneration (nAMD) patients. We performed pooled DNA based GWAS on 285 anti-VEGF treated nAMD patients using high density Illumina 4.3 M array. Primary outcome was change in VA in Early Treatment Diabetic Retinopathy Study (ETDRS) letters after 6 months of anti-VEGF treatment (patients who lost ≥5 ETDRS letters classified as non-responders and all remaining classified as responders). GWAS analysis identified 44 SNPs of interest: 37 with strong evidence of association (p < 9 × 10−8), 2 in drug resistance genes (p < 5 × 10−6) and 5 nonsynonymous changes (p < 1 × 10−4). In the validation phase, individual genotyping of 44 variants showed three SNPs (rs4910623 p = 5.6 × 10−5, rs323085 p = 6.5 × 10−4 and rs10198937 p = 1.30 × 10−3) remained associated with VA response at 6 months. SNP rs4910623 also associated with treatment response at 3 months (p = 1.5 × 10−3). Replication of these three SNPs in 376 patients revealed association of rs4910623 with poor VA response after 3 and 6 months of treatment (p = 2.4 × 10−3 and p = 3.5 × 10−2, respectively). Meta-analysis of both cohorts (673 samples) confirmed association of rs4910623 with poor VA response after 3 months (p = 1.2 × 10−5) and 6 months (p = 9.3 × 10−6) of treatment in nAMD patients.
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Affiliation(s)
- Moeen Riaz
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Laura Lorés-Motta
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Andrea J Richardson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Yi Lu
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Grant Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amer Omar
- Montreal Retina Institute, Westmount, Canada
| | - Robert K Koenekoop
- Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - John Chen
- Department of Ophthalmology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Philipp Muether
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Lebriz Altay
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Dzenita Smailhodzic
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Freekje van Asten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS and Dept: Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Stuart MacGregor
- Statistical Genetics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Robyn H Guymer
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Paul N Baird
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Australia
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46
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Pule GD, Ngo Bitoungui VJ, Chetcha Chemegni B, Kengne AP, Wonkam A. Studies of novel variants associated with Hb F in Sardinians and Tanzanians in sickle cell disease patients from Cameroon. Hemoglobin 2016; 40:377-380. [PMID: 27829299 DOI: 10.1080/03630269.2016.1251453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High level of Hb F has been shown to improve survival in sickle cell disease. Among 453 Cameroonians with sickle cell disease, we have investigated 18 selected single-nucleotide polymorphisms (SNPs) in novel and suggestive loci associated with Hb F level identified through a genomewide association study in sickle cell disease patients in Tanzania, and whole-genome sequencing of a population from Sardinia. Seven of 10 variants reported in Sardinians were either monomorphic or very rare in the Cameroonians. No associations were observed with any SNPs and Hb F levels in Cameroonians affected by sickle cell disease. The present study illustrates the complexity of replicating Hb F-promoting variants association results across populations.
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Affiliation(s)
- Gift D Pule
- a Division of Human Genetics, Department of Pathology, Faculty of Health Sciences , University of Cape Town , Cape Town , South Africa
| | - Valentina J Ngo Bitoungui
- b Department of Microbiology, Hematology, Parasitology et de Infectious Pathologies, Faculty of Medicine and Biomedical Sciences , University of Yaoundé , Cameroon
| | - Bernard Chetcha Chemegni
- b Department of Microbiology, Hematology, Parasitology et de Infectious Pathologies, Faculty of Medicine and Biomedical Sciences , University of Yaoundé , Cameroon
| | - Andre P Kengne
- c Non-Communicable Diseases Research Unit, South African Medical Research Council , Cape Town , South Africa
| | - Ambroise Wonkam
- a Division of Human Genetics, Department of Pathology, Faculty of Health Sciences , University of Cape Town , Cape Town , South Africa
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47
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Vathipadiekal V, Farrell JJ, Wang S, Edward HL, Shappell H, Al-Rubaish A, Al-Muhanna F, Naserullah Z, Alsuliman A, Qutub HO, Simkin I, Farrer LA, Jiang Z, Luo HY, Huang S, Mostoslavsky G, Murphy GJ, Patra PK, Chui DH, Alsultan A, Al-Ali AK, Sebastiani P, Steinberg MH. A candidate transacting modulator of fetal hemoglobin gene expression in the Arab-Indian haplotype of sickle cell anemia. Am J Hematol 2016; 91:1118-1122. [PMID: 27501013 DOI: 10.1002/ajh.24527] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/30/2022]
Abstract
Fetal hemoglobin (HbF) levels are higher in the Arab-Indian (AI) β-globin gene haplotype of sickle cell anemia compared with African-origin haplotypes. To study genetic elements that effect HbF expression in the AI haplotype we completed whole genome sequencing in 14 Saudi AI haplotype sickle hemoglobin homozygotes-seven selected for low HbF (8.2% ± 1.3%) and seven selected for high HbF (23.5% ± 2.6%). An intronic single nucleotide polymorphism (SNP) in ANTXR1, an anthrax toxin receptor (chromosome 2p13), was associated with HbF. These results were replicated in two independent Saudi AI haplotype cohorts of 120 and 139 patients, but not in 76 Saudi Benin haplotype, 894 African origin haplotype and 44 AI haplotype patients of Indian origin, suggesting that this association is effective only in the Saudi AI haplotype background. ANTXR1 variants explained 10% of the HbF variability compared with 8% for BCL11A. These two genes had independent, additive effects on HbF and together explained about 15% of HbF variability in Saudi AI sickle cell anemia patients. ANTXR1 was expressed at mRNA and protein levels in erythroid progenitors derived from induced pluripotent stem cells (iPSCs) and CD34+ cells. As CD34+ cells matured and their HbF decreased ANTXR1 expression increased; as iPSCs differentiated and their HbF increased, ANTXR1 expression decreased. Along with elements in cis to the HbF genes, ANTXR1 contributes to the variation in HbF in Saudi AI haplotype sickle cell anemia and is the first gene in trans to HBB that is associated with HbF only in carriers of the Saudi AI haplotype. Am. J. Hematol. 91:1118-1122, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vinod Vathipadiekal
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - John J. Farrell
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Shuai Wang
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Heather L. Edward
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Heather Shappell
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - A.M. Al-Rubaish
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Z. Naserullah
- Al-Omran Scientific Chair for Hematological Diseases; King Faisal University; Al-Ahsa Kingdom of Saudi Arabia
- Department of Pediatrics; Maternity and Child Hospital; Dammam Kingdom of Saudi Arabia
| | - A. Alsuliman
- Alomran Scientific Chair; King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
| | - Hatem Othman Qutub
- Alomran Scientific Chair; King Faisal University; Al-Ahsa Kingdom of Saudi Arabia
| | - Irene Simkin
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Zhihua Jiang
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Hong-Yuan Luo
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Shengwen Huang
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Gustavo Mostoslavsky
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - George J. Murphy
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Pradeep K. Patra
- Department of Biochemistry; Pt. J. N. M. Medical College; Raipur Chattisgarh India
| | - David H.K. Chui
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics; College of Medicine, King Saud University; Riyadh Saudi Arabia
| | - Amein K. Al-Ali
- Center for Research and Medical Consultation; University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Paola Sebastiani
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Martin H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
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48
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Mnika K, Pule GD, Dandara C, Wonkam A. An Expert Review of Pharmacogenomics of Sickle Cell Disease Therapeutics: Not Yet Ready for Global Precision Medicine. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:565-574. [PMID: 27636225 PMCID: PMC5067801 DOI: 10.1089/omi.2016.0105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sickle cell disease (SCD) is a blood disease caused by a single nucleotide substitution (T > A) in the beta globin gene on chromosome 11. The single point mutation (Glu6Val) promotes polymerization of hemoglobin S (HbS) and causes sickling of erythrocytes. Vaso-occlusive painful crises are associated with recurrent and long-term use of analgesics/opioids and hydroxyurea (HU) by people living with SCD. The present analysis offers a state-of-the-art expert review of the effectiveness of pharmacogenomics/genetics of pain management in SCD, with specific focus on HU and opioids. The literature search used the following keywords: SCD, pharmacogenomics, pharmacogenetics, pain, antalgics, opioids, morphine, and HU. The literature was scanned until March 2016, with specific inclusion of targeted landmark and background articles on SCD. Surprisingly, our review identified only a limited number of studies that addressed the genetic/genomic basis of variable responses to pain (e.g., variants in OPRM1, HMOX-1, GCH1, VEGFA COMT genes), and pharmacogenomics of antalgics and opioids (e.g., variants in OPRM1, STAT6, ABCB1, and COMT genes) in SCD. There has been greater progress made toward identifying the key genomic variants, mainly in BCL11A, HBS1L-MYB, or SAR1, which contribute to response to HU treatment. However, the complete picture on pharmacogenomic determinants of the above therapeutic phenotypes remains elusive. Strikingly, no study has been conducted in sub-Saharan Africa where majority of the patients with SCD live. This alerts the broader global life sciences community toward the existing disparities in optimal and ethical targeting of research and innovation investments for SCD specifically and precision medicine and pharmacology research broadly.
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Affiliation(s)
- Khuthala Mnika
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Gift D. Pule
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
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49
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Sellgren CM, Kegel ME, Bergen SE, Ekman CJ, Olsson S, Larsson M, Vawter MP, Backlund L, Sullivan PF, Sklar P, Smoller JW, Magnusson PKE, Hultman CM, Walther-Jallow L, Svensson CI, Lichtenstein P, Schalling M, Engberg G, Erhardt S, Landén M. A genome-wide association study of kynurenic acid in cerebrospinal fluid: implications for psychosis and cognitive impairment in bipolar disorder. Mol Psychiatry 2016; 21:1342-50. [PMID: 26666201 PMCID: PMC4965332 DOI: 10.1038/mp.2015.186] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 01/14/2023]
Abstract
Elevated cerebrospinal fluid (CSF) levels of the glia-derived N-methyl-D-aspartic acid receptor antagonist kynurenic acid (KYNA) have consistently been implicated in schizophrenia and bipolar disorder. Here, we conducted a genome-wide association study based on CSF KYNA in bipolar disorder and found support for an association with a common variant within 1p21.3. After replication in an independent cohort, we linked this genetic variant-associated with reduced SNX7 expression-to positive psychotic symptoms and executive function deficits in bipolar disorder. A series of post-mortem brain tissue and in vitro experiments suggested SNX7 downregulation to result in a caspase-8-driven activation of interleukin-1β and a subsequent induction of the brain kynurenine pathway. The current study demonstrates the potential of using biomarkers in genetic studies of psychiatric disorders, and may help to identify novel drug targets in bipolar disorder.
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Affiliation(s)
- C M Sellgren
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - M E Kegel
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - S E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - C J Ekman
- Section of Psychiatry, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - S Olsson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - M Larsson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - M P Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine School of Medicine, Irvine, CA, USA
| | - L Backlund
- Neurogenetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - P F Sullivan
- Department of Genetic and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - P Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics, Research, Massachusetts General Hospital, Boston, MA, USA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - P K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - C M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - L Walther-Jallow
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - C I Svensson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - P Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - M Schalling
- Neurogenetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - G Engberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - S Erhardt
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - M Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,The Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden,Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg SE-413 45, Sweden. E-mail:
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Reyes-Gibby CC, Wang J, Silvas MRT, Yu RK, Hanna EY, Shete S. Genome-wide association study suggests common variants within RP11-634B7.4 gene influencing severe pre-treatment pain in head and neck cancer patients. Sci Rep 2016; 6:34206. [PMID: 27670397 PMCID: PMC5037456 DOI: 10.1038/srep34206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/09/2016] [Indexed: 12/20/2022] Open
Abstract
Pain is often one of the first signs of squamous cell carcinoma of the head and neck (HNSCC). Pain at diagnosis is an important prognostic marker for the development of chronic pain, and importantly, for the overall survival time. To identify variants influencing severe pre-treatment pain in 1,368 patients newly diagnosed with HNSCC, we conducted a genome-wide association study based on 730,525 tagging SNPs. The patients were all previously untreated for cancer. About 15% of the patients had severe pre-treatment pain, defined as pain score ≥7 (0 = “no pain” and 10 = “worst pain”). We identified 3 common genetic variants in high linkage disequilibrium for severe pre-treatment pain, representing one genomic region at 1q44 (rs3862188, P = 3.45 × 10−8; rs880143, P = 3.45 × 10−8; and rs7526880, P = 4.92 × 10−8), which maps to the RP11-634B7.4 gene, a novel antisense gene to three olfactory receptor genes. Olfactory receptor genes, upstream effectors of the MAPK signaling cascade, might be novel target genes for pain in HNSCC patients. Future experimental validation to explore biological mechanisms will be key to defining the role of the intronic variants and non-coding RNA for pain in patients with HNSCC.
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Affiliation(s)
- Cielito C Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mary Rose T Silvas
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Robert K Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ehab Y Hanna
- Department of Head &Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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