1
|
Bard AM, Clark LV, Cosgun E, Aldinger KA, Timms A, Quina LA, Ferres JML, Jardine D, Haas EA, Becker TM, Pagan CM, Santani A, Martinez D, Barua S, McNutt Z, Nesbitt A, Mitchell EA, Ramirez JM. Known pathogenic gene variants and new candidates detected in sudden unexpected infant death using whole genome sequencing. Am J Med Genet A 2024:e63596. [PMID: 38895864 DOI: 10.1002/ajmg.a.63596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 06/21/2024]
Abstract
The purpose of this study is to gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Whole Genome Sequencing (WGS) was performed on 144 infants that succumbed to SUID, and 573 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Variants of interest were identified in 88 genes, in 64.6% of our cohort. Seventy-three of these have been previously associated with SIDS/SUID/SUDP. Forty-three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders and in two genes associated with immunological function. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy-two infants met the triple risk hypothesis criteria. Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID.
Collapse
Affiliation(s)
- Angela M Bard
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lindsay V Clark
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Erdal Cosgun
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- AI for Good Research Lab, Microsoft, Redmond, Washington, USA
- Microsoft Genomics Team, Redmond, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew Timms
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lely A Quina
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Juan M Lavista Ferres
- Bioinformatics and Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
- AI for Good Research Lab, Microsoft, Redmond, Washington, USA
- Microsoft Genomics Team, Redmond, Washington, USA
| | - David Jardine
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elisabeth A Haas
- Department of Research, Rady Children's Hospital-San Diego, San Diego, California, USA
| | - Tatiana M Becker
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Chelsea M Pagan
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | | | | | | | | | | | - Edwin A Mitchell
- Department of Paediatrics, University of Auckland, Auckland, New Zealand
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, USA
| |
Collapse
|
2
|
Leninsky MA, Sobolev VE, Sokolova MO, Voitenko NG, Skvortsov NV. Quantification of 11 metabolites in rat urine after exposure to organophosphates. Lab Anim Res 2024; 40:23. [PMID: 38845041 PMCID: PMC11155157 DOI: 10.1186/s42826-024-00209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The aim of the study was to develop a technique for quantitative determination of rat urine metabolites by HPLC-MS/MS, which can be used to search for biomarkers of acute intoxication with organophosphates (OPs). RESULTS The content of metabolites in the urine of rats exposed to a single dose of paraoxon (POX1x); interval, twice daily administration of paraoxon (POX2x); exposure to 2-(o-cresyl)-4H-1, 3, 2-benzodioxaphosphorin-2-oxide and paraoxon (CBPOX) was investigated. New data were obtained on the content in the urine of intact rats as well as rats in 3 models of OP poisoning: 3-methylhistidine, threonine, creatine, creatinine, lactic acid, acetylcarnitine, inosine, hypoxanthine, adenine, 3-hydroxymethyl-butyrate and 2-hydroxymethyl-butyrate. CONCLUSIONS The proposed assay procedure is a simple and reliable tool for urine metabolomic studies. Within 1-3 days after OP exposure in all three models of acute intoxication, the concentration of metabolites in rat urine, with the exception of adenine, changes similarly and symmetrically, regardless of the method of poisoning modeling, in all three models of acute intoxication. Further studies are needed to determine the specificity and reliability of using urinary metabolite concentration changes as potential biomarkers of acute organophosphate intoxication.
Collapse
Affiliation(s)
- Michael A Leninsky
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez 44, St. Petersburg, 194223, Russia
| | - Vladislav E Sobolev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez 44, St. Petersburg, 194223, Russia.
| | - Margarita O Sokolova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez 44, St. Petersburg, 194223, Russia
| | - Natalya G Voitenko
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Thorez 44, St. Petersburg, 194223, Russia
| | - Nikita V Skvortsov
- Federal State Budgetary Scientific Institution "Institute of Experimental Medicine", 12, Acad. Pavlov Street, St. Petersburg, 197022, Russia
| |
Collapse
|
3
|
Bard AM, Clark LV, Cosgun E, Aldinger KA, Timms A, Quina LA, Lavista Ferres JM, Jardine D, Haas EA, Becker TM, Pagan CM, Santani A, Martinez D, Barua S, McNutt Z, Nesbitt A, Mitchell EA, Ramirez JM. Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death using Whole Genome Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.11.23295207. [PMID: 37745463 PMCID: PMC10516094 DOI: 10.1101/2023.09.11.23295207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Purpose To gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Methods Whole Genome Sequencing (WGS) was performed on 145 infants that succumbed to SUID, and 576 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Results Variants of interest were identified in 86 genes, 63.4% of our cohort. Seventy-one of these have been previously associated with SIDS/SUID/SUDP. Forty-three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy-two infants met the triple risk hypothesis criteria (Figure 1). Conclusion Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID.
Collapse
|
4
|
Siren PMA. SIDS-CDF hypothesis revisited: explaining hypoxia in SIDS. Ups J Med Sci 2016; 121:199-201. [PMID: 27460606 PMCID: PMC4967269 DOI: 10.1080/03009734.2016.1176972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/30/2016] [Accepted: 04/06/2016] [Indexed: 01/24/2023] Open
|
5
|
Jones KL, Krous HF, Nadeau J, Blackbourne B, Zielke HR, Gozal D. Vascular endothelial growth factor in the cerebrospinal fluid of infants who died of sudden infant death syndrome: evidence for antecedent hypoxia. Pediatrics 2003; 111:358-63. [PMID: 12563064 DOI: 10.1542/peds.111.2.358] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Recurrent hypoxemia has been proposed as an important pathophysiological mechanism underlying sudden infant death syndrome (SIDS). However, conflicting results emerged when xanthines were used as markers for hypoxia. The vascular endothelial growth factor (VEGF) gene is highly sensitive to changes in tissue partial oxygen tension, and changes in genomic and protein expression occur even after changes in oxygenation within the physiologic range. METHODS For determining whether hypoxia precedes SIDS, VEGF levels were measured using an enzyme-linked immunosorbent assay in the cerebrospinal fluid (CSF) of 51 SIDS infants and in 33 additional control infants who died of an identifiable cause. In addition, 6 rats that had a chronically implanted catheter in the lateral ventricle were exposed to a short hypoxic challenge, and VEGF concentrations were measured in CSF at various time points for 24 hours. Another set of 6 rats were killed with a pentobarbital overdose, and VEGF CSF levels were obtained at different time points after death. RESULTS Mean VEGF concentrations in CSF were 308.2 +/- 299.1 pg/dL in the SIDS group and 85.1 +/- 82.9 pg/dL in those who died of known causes. Mean postmortem delay averaged 22 hours for both groups. In rat experiments, hypoxic exposures induced time-dependent increases in VEGF, peaking at 12 hours and returning to baseline at 24 hours. Postmortem duration in the animals was associated with gradual increases in VEGF that reached significance only at 36 hours. CONCLUSIONS We conclude that VEGF CSF concentrations are significantly higher in infants who die of SIDS. We postulate that hypoxia is a frequent event that precedes the sudden and unexpected death of these infants.
Collapse
Affiliation(s)
- Kimberly L Jones
- Kosair Children's Hospital Research Institute, Department of Pediatrics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | | | | | | | | | | |
Collapse
|
6
|
Côté A, Barter J, Meehan B. Age-dependent metabolic effects of repeated hypoxemia in piglets. Can J Physiol Pharmacol 2000. [DOI: 10.1139/y99-141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to determine whether repeated exposure to hypoxemia would modify the response to hypoxemia during maturation. We exposed piglets to three 1-h cycles of hypoxemia (PaO2 = 30 to 35 mmHg; 1 mmHg = 133.3 Pa) at 1 week (n = 9), 2-3 weeks (n = 10), and 4-5 weeks of age (n = 10). O2 consumption (VO2) and CO2 production (VCO2) were measured, and alveolar ventilation (VA) was derived from VCO2 and PaCO2. Levels of lactic acid (lactate) and serum catecholamines were also measured. With hypoxemia, time had a significant effect on VO2 and body temperature in an age-dependent fashion: that is, whereas the 1 week group and the 4-5 week group showed both variables decreasing over time, the 2-3 week group showed no drop in VO2 and a small increase in body temperature over time. Lactate levels increased with hypoxemia in all animals during the first exposure. However, with repeated exposures to hypoxemia, only the 2-3 week group continued to increase its lactate levels. Furthermore, the changes in lactate levels paralleled the changes in epinephrine levels with hypoxemia. We found, too, that although VA increased significantly with hypoxemia in all animals, this change was not modified by age or repeated exposures. No significant effects of age or repeated exposures were found in the cardiovascular response to hypoxemia. We concluded that, from a metabolic viewpoint, after repeated exposures to hypoxemia the 2-3 week animals responded differently.Key words: metabolic rate, lactic acid, maturation, catecholamines.
Collapse
|
7
|
Opdal SH, Rognum TO, Vege A, Saugstad OD. Hypoxanthine levels in vitreous humor: a study of influencing factors in sudden infant death syndrome. Pediatr Res 1998; 44:192-6. [PMID: 9702913 DOI: 10.1203/00006450-199808000-00009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Elevated hypoxanthine (Hx) levels in the vitreous humor of victims of the sudden infant death syndrome (SIDS) have been been claimed to indicate hypoxia before death. An important methodologic problem is the temperature-dependent Hx increase after death. Although most previous studies have corrected for expected postmortem Hx increase, the aim of the present study was to omit this problem by matching the subjects of the different groups studied for similar postmortem time. Thirteen cases of violent death, 11 cases of borderline SIDS, 22 cases of death from infectious disease, and 17 cases of death from heart/lung disease were compared with a 3-fold number of SIDS cases. To investigate the impact of environmental factors on the Hx levels of the SIDS cases, the following possible confounding factors were investigated: attempt to resuscitate, slight infections before death, sleeping position, and time of the day when found dead. To investigate whether the size of the eyeball would influence the Hx level, five cases of violent death in children were compared with 15 adults who died suddenly. The vitreous humor Hx level was significantly higher in SIDS victims than in cases of violent death (p < 0.01) and deaths due to heart/lung disease (p < 0.01), whereas no such difference was found either between SIDS and borderline SIDS or SIDS and infectious death. There were no differences between any of the subgroups of SIDS victims. The vitreous humor Hx level in small children and adults did not differ. The findings raise the question of possible similarities in death mechanism in SIDS and infectious death.
Collapse
Affiliation(s)
- S H Opdal
- Institute of Forensic Medicine, University of Oslo, The National Hospital, Norway
| | | | | | | |
Collapse
|
8
|
Almaas R, Sundar TB, Rootwelt T, Oyasaeter S, Saugstad OD. Plasma hypoxanthine reacts more abruptly to changes in oxygenation than base deficit and uric acid in newborn piglets. J Perinat Med 1997; 25:353-60. [PMID: 9350606 DOI: 10.1515/jpme.1997.25.4.353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Previously, high postmortem concentrations of hypoxanthine have been found in vitreous humor of children dying from sudden infant death syndrome (SIDS). We wanted to investigate further the accumulation of hypoxanthine in vitreous humor during hypoxia. Twenty-four piglets aged 9-15 days were exposed to continuous hypoxemia (180 min 11% O2, n = 6), long interval intermittent hypoxemia (60 min 11% O2, 20 min room air, n = 7) or short interval intermittent hypoxemia (10 min 9% O2, 10 min room air with (n = 6) or without (n = 5) superimposed ligation of both carotid arteries). The increase in vitreous humor Hyp was four-fold higher (p < 0.01) with ligation of the carotid arteries (14 +/- 2.4 to 38 +/- 8.9 mumol/l) than without ligation (15 +/- 2.8 to 21 +/- 5.9 mumol/l). During continuous hypoxemia, plasma Hyp (r = 0.85), Xa (r = 0.89) uric acid (UA) (r = 0.85), and base deficit (BD) (r = 0.78) increased almost linearly (p < 0.001). Plasma Hyp responded more abruptly to changes in oxygenation than base deficit (BD) and UA. Ligation of the carotid arteries had a strong impact on Hyp accumulation in vitreous humor, suggesting that vitreous humor Hyp is not merely a filtration product of plasma Hyp, but reflects local hypoxia/ischemia in the eye.
Collapse
Affiliation(s)
- R Almaas
- Department of Pediatric Research, National Hospital, Rikshospitalet, Oslo, Norway
| | | | | | | | | |
Collapse
|
9
|
Waters KA, Beardsmore CS, Paquette J, Meehan B, Côté A, Moss IR. Respiratory responses to rapid-onset, repetitive vs. continuous hypoxia in piglets. RESPIRATION PHYSIOLOGY 1996; 105:135-42. [PMID: 8897659 DOI: 10.1016/0034-5687(96)00046-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Repeated, frequent hypoxic exposures may precede Sudden Infant Death. This study assessed whether such hypoxic modality, vs. continuous hypoxia, compromised compensatory cardiorespiratory responses. Following aseptic, chronic instrumentation, 10 to 20 day-old, unsedated piglets underwent measurements of arterial O2 saturation, pH and gas tensions, respiration, heart rate, physical activity, O2 consumption and rectal temperature on several experimental days. The piglets were exposed to 21 min of either 10% or 6% O2 in N2, each comprising either seven, 3-min exposures alternating with 3-min intervals in 21% O2 balance N2, or 7 consecutive hypoxic exposures. Responses to 6% hypoxia were greater than those to 10% hypoxia. In 10% hypoxia, responses to repetitive vs. continuous exposure differed only in PaCO2. In 6% hypoxia, repetitive vs. continuous exposure resulted in lower respiratory frequency (p < 0.05) and in lower ventilation equivalent (p = 0.07) despite higher activity levels. Thus, the mode of hypoxic exposure determines the extent of the respiratory response: Severe, repetitive hypoxia mitigates protective respiratory responses when compared to equivalent, but sustained hypoxia.
Collapse
Affiliation(s)
- K A Waters
- Department of Pediatrics, McGill University, Montreal, Que, Canada
| | | | | | | | | | | |
Collapse
|
10
|
Kock R, Delvoux B, Sigmund M, Greiling H. A comparative study of the concentrations of hypoxanthine, xanthine, uric acid and allantoin in the peripheral blood of normals and patients with acute myocardial infarction and other ischaemic diseases. EUROPEAN JOURNAL OF CLINICAL CHEMISTRY AND CLINICAL BIOCHEMISTRY : JOURNAL OF THE FORUM OF EUROPEAN CLINICAL CHEMISTRY SOCIETIES 1994; 32:837-42. [PMID: 7888480 DOI: 10.1515/cclm.1994.32.11.837] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The aim of this study was the elucidation of the role of the xanthine oxidoreductase in the purine metabolism in ischaemic diseases of man. The serum concentrations of hypoxanthine, xanthine, uric acid and allantoin were determined in peripheral blood samples from patients with angina pectoris, cerebral insult and myocardial infarction with thrombolytic therapy and were compared with the concentrations obtained for healthy males and females. No significant differences were observed for the serum hypoxanthine concentrations, xanthine concentrations, the sum (hypoxanthine+xanthine) and the ratio (xanthine/hypoxanthine) between the healthy males, healthy females, the patients suffering from angina pectoris and the patients suffering from cerebral insult. An increase of the serum xanthine concentration in patients with myocardial infarction indicates a significant metabolic involvement of xanthine oxidoreductase in this disease and therefore a possible role in the development of tissue damage in the postischaemic phase due to oxygen radicals generated by the oxidase activity of this enzyme. The serum concentrations of uric acid and allantoin showed no differences between any of the studied groups. Study of the non-enzymatic oxidation of uric acid to allantoin by oxygen radicals, a relevant radical-scavenging mechanism in other diseases, provided no indication of an increased concentration of oxygen radicals due to the xanthine oxidoreductase reaction or other radical-producing mechanisms.
Collapse
Affiliation(s)
- R Kock
- Institute for Clinical Chemistry and Pathobiochemistry, Medical Faculty, University of Technology Aachen, Germany
| | | | | | | |
Collapse
|