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Hernandez-Beeftink T, Guillen-Guio B, Lorenzo-Salazar JM, Corrales A, Suarez-Pajes E, Feng R, Rubio-Rodríguez LA, Paynton ML, Cruz R, García-Laorden MI, Prieto-González M, Rodríguez-Pérez A, Carriedo D, Blanco J, Ambrós A, González-Higueras E, Espinosa E, Muriel A, Tamayo E, Martin MM, Lorente L, Domínguez D, de Lorenzo AG, Giannini HM, Reilly JP, Jones TK, Añón JM, Soro M, Carracedo Á, Wain LV, Meyer NJ, Villar J, Flores C. A genome-wide association study of survival in patients with sepsis. Crit Care 2022; 26:341. [PMID: 36335405 PMCID: PMC9637317 DOI: 10.1186/s13054-022-04208-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction and has a high mortality rate in adult intensive care units. Most genetic studies have identified gene variants associated with development and outcomes of sepsis focusing on biological candidates. We conducted the first genome-wide association study (GWAS) of 28-day survival in adult patients with sepsis. METHODS This study was conducted in two stages. The first stage was performed on 687 European sepsis patients from the GEN-SEP network and 7.5 million imputed variants. Association testing was conducted with Cox regression models, adjusting by sex, age, and the main principal components of genetic variation. A second stage focusing on the prioritized genetic variants was performed on 2,063 ICU sepsis patients (1362 European Americans and 701 African-Americans) from the MESSI study. A meta-analysis of results from the two stages was conducted and significance was established at p < 5.0 × 10-8. Whole-blood transcriptomic, functional annotations, and sensitivity analyses were evaluated on the identified genes and variants. FINDINGS We identified three independent low-frequency variants associated with reduced 28-day sepsis survival, including a missense variant in SAMD9 (hazard ratio [95% confidence interval] = 1.64 [1.37-6.78], p = 4.92 × 10-8). SAMD9 encodes a possible mediator of the inflammatory response to tissue injury. INTERPRETATION We performed the first GWAS of 28-day sepsis survival and identified novel variants associated with reduced survival. Larger sample size studies are needed to better assess the genetic effects in sepsis survival and to validate the findings.
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Affiliation(s)
- Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
| | - Rui Feng
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Raquel Cruz
- Genomic Medicine Group, Biomedical Research Center of Rare Diseases (CIBERER), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Isabel García-Laorden
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Aurelio Rodríguez-Pérez
- Department of Anesthesiology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Department of Medical and Surgical Sciences, University of Las Palmas de Gran Canaria, Gran Canaria, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Hospitalario Universitario de León, León, Spain
| | - Jesús Blanco
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Alfonso Ambrós
- Intensive Care Unit, Hospital General de Ciudad Real, Ciudad Real, Spain
| | | | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Arturo Muriel
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Eduardo Tamayo
- CIBER de Enfermedades Infecciosas, Department of Anesthesiology and Resuscitation, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
- Departamento de Cirugía, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - María M Martin
- Intensive Care Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Leonardo Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
| | - David Domínguez
- Department of Anesthesiology, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Heather M Giannini
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - John P Reilly
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - José M Añón
- Intensive Care Unit, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Marina Soro
- Department of Anesthesiology, Hospital Clinico Universitario de Valencia, Valencia, Spain
| | - Ángel Carracedo
- Genomic Medicine Group, Biomedical Research Center of Rare Diseases (CIBERER), University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomic Medicine Group, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain
- Galician Foundation of Genomic Medicine, Foundation of Health Research Institute of Santiago de Compostela (FIDIS), SERGAS, Santiago de Compostela, Spain
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- Leicester Respiratory Biomedical Research, Centre, National Institute for Health Research, Glenfield Hospital, Leicester, UK
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain.
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain.
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Suntharalingham JP, Ishida M, Del Valle I, Stalman SE, Solanky N, Wakeling E, Moore GE, Achermann JC, Buonocore F. Emerging phenotypes linked to variants in SAMD9 and MIRAGE syndrome. Front Endocrinol (Lausanne) 2022; 13:953707. [PMID: 36060959 PMCID: PMC9433874 DOI: 10.3389/fendo.2022.953707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Heterozygous de novo variants in SAMD9 cause MIRAGE syndrome, a complex multisystem disorder involving Myelodysplasia, Infection, Restriction of growth, Adrenal hypoplasia, Genital phenotypes, and Enteropathy. The range of additional clinical associations is expanding and includes disrupted placental development, poor post-natal growth and endocrine features. Increasingly, milder phenotypic features such as hypospadias in small for gestational age (SGA) boys and normal adrenal function are reported. Some children present with isolated myelodysplastic syndrome (MDS/monosomy 7) without MIRAGE features. Objective We aimed to investigate: 1) the range of reported SAMD9 variants, clinical features, and possible genotype-phenotype correlations; 2) whether SAMD9 disruption affects placental function and leads to pregnancy loss/recurrent miscarriage (RM); 3) and if pathogenic variants are associated with isolated fetal growth restriction (FGR). Methods Published data were analyzed, particularly reviewing position/type of variant, pregnancy, growth data, and associated endocrine features. Genetic analysis of SAMD9 was performed in products of conception (POC, n=26), RM couples, (couples n=48; individuals n=96), children with FGR (n=44), SGA (n=20), and clinical Silver-Russell Syndrome (SRS, n=8), (total n=194). Results To date, SAMD9 variants are reported in 116 individuals [MDS/monosomy 7, 64 (55.2%); MIRAGE, 52 (44.8%)]. Children with MIRAGE features are increasingly reported without an adrenal phenotype (11/52, 21.2%). Infants without adrenal dysfunction were heavier at birth (median 1515 g versus 1020 g; P < 0.05) and born later (median 34.5 weeks versus 31.0; P < 0.05) compared to those with adrenal insufficiency. In MIRAGE patients, hypospadias is a common feature. Additional endocrinopathies include hypothyroidism, hypo- and hyper-glycemia, short stature and panhypopituitarism. Despite this increasing range of phenotypes, genetic analysis did not reveal any likely pathogenic variants/enrichment of specific variants in SAMD9 in the pregnancy loss/growth restriction cohorts studied. Conclusion MIRAGE syndrome is more phenotypically diverse than originally reported and includes growth restriction and multisystem features, but without adrenal insufficiency. Endocrinopathies might be overlooked or develop gradually, and may be underreported. As clinical features including FGR, severe infections, anemia and lung problems can be non-specific and are often seen in neonatal medicine, SAMD9-associated conditions may be underdiagnosed. Reaching a specific diagnosis of MIRAGE syndrome is critical for personalized management.
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Affiliation(s)
- Jenifer P. Suntharalingham
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ignacio Del Valle
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Susanne E. Stalman
- Department of Pediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Nita Solanky
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital, London, United Kingdom
| | - Gudrun E. Moore
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John C. Achermann
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Tanase-Nakao K, Kawai M, Wada K, Kagami M, Narumi S. Acquired uniparental disomy of chromosome 7 in a patient with MIRAGE syndrome that veiled a pathogenic SAMD9 variant. Clin Pediatr Endocrinol 2021; 30:163-169. [PMID: 34629738 PMCID: PMC8481078 DOI: 10.1297/cpe.30.163] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/16/2021] [Indexed: 11/12/2022] Open
Abstract
Gain-of-function variants in SAMD9, which resides on chromosome 7, cause
MIRAGE syndrome that is associated with congenital adrenal insufficiency and gonadal
dysgenesis. We previously reported a Japanese patient with MIRAGE syndrome carrying a
de novo heterozygous SAMD9 variant (p.Ala1479Ser). In
this study, we confirmed the pathogenicity of Ala1479Ser-SAMD9 in vitro.
Genetic study results revealed an atypically low variant allele frequency (26%) and we
suspected of genomic rearrangement(s) involving chromosome 7. Single nucleotide
polymorphism (SNP) array and short tandem repeat analysis showed presence of mosaic
maternal isodisomic uniparental disomy 7 (UPD7). Deep sequencing using DNA samples
obtained at 0, 6, 10, and 25 mo of age revealed that the percentage of cells with UPD7
increased constantly from 6% to 82% over 25 mo, and this increase coincided with a
decrease in the percentage of cells with p.Ala1479Ser from 94% to nearly undetectable
levels. We further screened for low-allele-frequency and rare SAMD9
variants in eight patients with Silver-Russel syndrome and maternal UPD7; however, none of
the patients harbored such a variant. In conclusion, our case demonstrates that genetic
findings can vary considerably in patients with MIRAGE syndrome and that a comprehensive
diagnostic approach, including SNP array and deep sequencing, is important in such
cases.
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Affiliation(s)
- Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masanobu Kawai
- Department of Gastroenterology, Nutrition and Endocrinology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazuko Wada
- Department of Neonatology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Zhang S, Qiao Y, Wang Z, Zhuang J, Sun Y, Shang X, Li G. Identification of novel compound heterozygous variants in SLC19A2 and the genotype-phenotype associations in thiamine-responsive megaloblastic anemia. Clin Chim Acta 2021; 516:157-168. [PMID: 33571483 DOI: 10.1016/j.cca.2021.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND AND AIMS Thiamine-responsive megaloblastic anemia (TRMA), caused by SLC19A2 loss-of-function variants, is characterized by the triad of megaloblastic anemia, progressive sensorineural deafness, and non-type 1 diabetes mellitus. Here, we present the case of a Chinese infant with two novel variants segregating in compound heterozygous form in SLC19A2 and reviewed genotype-phenotype associations (GPAs) in patients with TRMA. MATERIALS AND METHODS Whole-exome sequencing was performed to establish a genetic diagnosis. The clinical manifestations and genetic variants were collected by performing a literature review. The bioinformatics software SIFT, PolyPhen2, and Mutation Taster was applied to predict variant effects and analyze GPAs. RESULTS Two novel variants segregating in compound heterozygous form in SLC19A2 (NM_006996.2: exon2:c.336_363del:p.W112fs; exon2:c.358G>T:p.G120X) was identified. Thiamine supplementation corrected anemia and diabetes mellitus but did not improve the hearing defect. In the literature, 183 patients with TRMA with 74 variants in SLC19A2 have been reported, with high incidence in the Middle East, South Asia, and the northern Mediterranean. Patients with biallelic premature termination codon variants presented with more severe phenotypes, and truncating sites on extracellular domains was a protective factor for the hemoglobin level at diagnosis. CONCLUSION Two novel compound heterozygous variants (NM_006996.2: exon2:c.336_363del:p.W112fs; exon2:c.358G>T:p.G120X) were identified, and GPAs in TRMA indicated the predictability of clinical manifestations.
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Affiliation(s)
- Shule Zhang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Yu Qiao
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Zengmin Wang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Jianxin Zhuang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Yan Sun
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Xiaohong Shang
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
| | - Guimei Li
- Department of Pediatric Endocrinology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China; Department of Pediatric Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677 Jingshi Road, Lixia Area, Jinan, Shandong 250021, China.
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