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Camiolo S, Hughes J, Baldanti F, Furione M, Lilleri D, Lombardi G, Angelini M, Gerna G, Zavattoni M, Davison AJ, Suárez NM. Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus Evol 2022; 8:veac114. [PMID: 37091479 PMCID: PMC10120596 DOI: 10.1093/ve/veac114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding the intrahost evolution of viral populations has implications in pathogenesis, diagnosis, and treatment and has recently made impressive advances from developments in high-throughput sequencing. However, the underlying analyses are very sensitive to sources of bias, error, and artefact in the data, and it is important that these are addressed adequately if robust conclusions are to be drawn. The key factors include (1) determining the number of viral strains present in the sample analysed; (2) monitoring the extent to which the data represent these strains and assessing the quality of these data; (3) dealing with the effects of cross-contamination; and (4) ensuring that the results are reproducible. We investigated these factors by generating sequence datasets, including biological and technical replicates, directly from clinical samples obtained from a small cohort of patients who had been infected congenitally with the herpesvirus human cytomegalovirus, with the aim of developing a strategy for identifying high-confidence intrahost variants. We found that such variants were few in number and typically present in low proportions and concluded that human cytomegalovirus exhibits a very low level of intrahost variability. In addition to clarifying the situation regarding human cytomegalovirus, our strategy has wider applicability to understanding the intrahost variability of other viruses.
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Affiliation(s)
- Salvatore Camiolo
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Joseph Hughes
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, School of Infection and Immunity, University of Pavia, Pavia 27100, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Milena Furione
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Daniele Lilleri
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Giuseppina Lombardi
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Micol Angelini
- Neonatal and Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Giuseppe Gerna
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Maurizio Zavattoni
- Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia 27100, Italy
| | - Andrew J Davison
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nicolás M Suárez
- School of Infection and Immunity, MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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van de Wal MAE, Adjobo-Hermans MJW, Keijer J, Schirris TJJ, Homberg JR, Wieckowski MR, Grefte S, van Schothorst EM, van Karnebeek C, Quintana A, Koopman WJH. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain 2022. [PMID: 34849584 DOI: 10.1093/brain/awab426%jbrain] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases. With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (complex I) induce isolated complex I deficiency and Leigh syndrome. This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA-encoded NDUFS4 gene, encoding the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) of complex I, induce 'mitochondrial complex I deficiency, nuclear type 1' (MC1DN1) and Leigh syndrome in paediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the Leigh syndrome pathomechanism and intervention testing. Here, we review and discuss the role of complex I and NDUFS4 mutations in human mitochondrial disease, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/Leigh syndrome pathomechanism and its therapeutic targeting.
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Affiliation(s)
- Melissa A E van de Wal
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | | | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom J J Schirris
- Department of Pharmacology and Toxicology, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Clara van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
- Department of Pediatrics, Emma Personalized Medicine Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Human Genetics, Emma Personalized Medicine Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Albert Quintana
- Mitochondrial Neuropathology Laboratory, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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West PJ, Thomson K, Billingsley P, Pruess T, Rueda C, Saunders GW, Smith MD, Metcalf CS, Wilcox KS. Spontaneous recurrent seizures in an intra-amygdala kainate microinjection model of temporal lobe epilepsy are differentially sensitive to antiseizure drugs. Exp Neurol 2022; 349:113954. [PMID: 34922908 PMCID: PMC8815304 DOI: 10.1016/j.expneurol.2021.113954] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 10/14/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
The discovery and development of novel antiseizure drugs (ASDs) that are effective in controlling pharmacoresistant spontaneous recurrent seizures (SRSs) continues to represent a significant unmet clinical need. The Epilepsy Therapy Screening Program (ETSP) has undertaken efforts to address this need by adopting animal models that represent the salient features of human pharmacoresistant epilepsy and employing these models for preclinical testing of investigational ASDs. One such model that has garnered increased interest in recent years is the mouse variant of the Intra-Amygdala Kainate (IAK) microinjection model of mesial temporal lobe epilepsy (MTLE). In establishing a version of this model, several methodological variables were evaluated for their effect(s) on pertinent quantitative endpoints. Although administration of a benzodiazepine 40 min after kainate (KA) induced status epilepticus (SE) is commonly used to improve survival, data presented here demonstrates similar outcomes (mortality, hippocampal damage, latency periods, and 90-day SRS natural history) between mice given midazolam and those that were not. Using a version of this model that did not interrupt SE with a benzodiazepine, a 90-day natural history study was performed and survival, latency periods, SRS frequencies and durations, and SRS clustering data were quantified. Finally, an important step towards model adoption is to assess the sensitivities or resistances of SRSs to a panel of approved and clinically used ASDs. Accordingly, the following ASDs were evaluated for their effects on SRSs in these mice: phenytoin (20 mg/kg, b.i.d.), carbamazepine (30 mg/kg, t.i.d.), valproate (240 mg/kg, t.i.d.), diazepam (4 mg/kg, b.i.d.), and phenobarbital (25 and 50 mg/kg, b.i.d.). Valproate, diazepam, and phenobarbital significantly attenuated SRS frequency relative to vehicle controls at doses devoid of observable adverse behavioral effects. Only diazepam significantly increased seizure freedom. Neither phenytoin nor carbamazepine significantly altered SRS frequency or freedom under these experimental conditions. These data demonstrate that SRSs in this IAK model of MTLE are pharmacoresistant to two representative sodium channel-inhibiting ASDs (phenytoin and carbamazepine) and partially sensitive to GABA receptor modulating ASDs (diazepam and phenobarbital) or a mixed-mechanism ASD (valproate). Accordingly, this model is being incorporated into the NINDS-funded ETSP testing platform for treatment resistant epilepsy.
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Affiliation(s)
- Peter J West
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA; Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA; Interdepartmental Neuroscience Program, University of Utah, Salt Lake City, UT 84108, USA.
| | - Kyle Thomson
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA; Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Peggy Billingsley
- Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Timothy Pruess
- Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Carlos Rueda
- Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Gerald W Saunders
- Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Misty D Smith
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA; Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA; School of Dentistry, University of Utah, Salt Lake City, UT 84108, USA
| | - Cameron S Metcalf
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA; Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA
| | - Karen S Wilcox
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA; Epilepsy Therapy Screening Program (ETSP) Contract Site, University of Utah, Salt Lake City, UT 84112, USA; Interdepartmental Neuroscience Program, University of Utah, Salt Lake City, UT 84108, USA
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van de Wal M, Adjobo-Hermans M, Keijer J, Schirris T, Homberg J, Wieckowski MR, Grefte S, van Schothorst EM, van Karnebeek C, Quintana A, Koopman WJH. Ndufs4 knockout mouse models of Leigh syndrome: pathophysiology and intervention. Brain 2021; 145:45-63. [PMID: 34849584 PMCID: PMC8967107 DOI: 10.1093/brain/awab426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondria are small cellular constituents that generate cellular energy (ATP) by oxidative phosphorylation (OXPHOS). Dysfunction of these organelles is linked to a heterogeneous group of multisystemic disorders, including diabetes, cancer, ageing-related pathologies and rare mitochondrial diseases. With respect to the latter, mutations in subunit-encoding genes and assembly factors of the first OXPHOS complex (complex I) induce isolated complex I deficiency and Leigh syndrome. This syndrome is an early-onset, often fatal, encephalopathy with a variable clinical presentation and poor prognosis due to the lack of effective intervention strategies. Mutations in the nuclear DNA-encoded NDUFS4 gene, encoding the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) of complex I, induce ‘mitochondrial complex I deficiency, nuclear type 1’ (MC1DN1) and Leigh syndrome in paediatric patients. A variety of (tissue-specific) Ndufs4 knockout mouse models were developed to study the Leigh syndrome pathomechanism and intervention testing. Here, we review and discuss the role of complex I and NDUFS4 mutations in human mitochondrial disease, and review how the analysis of Ndufs4 knockout mouse models has generated new insights into the MC1ND1/Leigh syndrome pathomechanism and its therapeutic targeting.
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Affiliation(s)
- Melissa van de Wal
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Merel Adjobo-Hermans
- Department of Biochemistry (286), RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | - Tom Schirris
- Department of Pharmacology and Toxicology, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands
| | - Judith Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Mariusz R Wieckowski
- Laboratory of Mitochondrial Biology and Metabolism, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Sander Grefte
- Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
| | | | - Clara van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Department of Pediatrics, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Albert Quintana
- Mitochondrial Neuropathology Laboratory, Institut de Neurociències and Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Werner J H Koopman
- Department of Pediatrics, Amalia Children's Hospital, RIMLS, RCMM, Radboudumc, Nijmegen, The Netherlands.,Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands
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Badanthadka M, D'Souza L, Salwa F. Strain specific response of mice to IMQ-induced psoriasis. J Basic Clin Physiol Pharmacol 2021; 32:959-968. [PMID: 33548169 DOI: 10.1515/jbcpp-2020-0112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/09/2020] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Psoriasis is an autoimmune, inflammatory disease that needs a reliable animal model. Imiquimod (IMQ)-induced psoriasis is a widely used preclinical tool for psoriasis research. However, this model is sensitive to the genetic variation of mice. The present study explores mice's genetic background on disease stability and severity induced by IMQ. METHODS Three distinct strains of mice (Balb/c, C57BL/6, and Swiss albino) were divided into four groups (Vaseline, IMQ, IMQ+Clobetasol, and IMQ+Curcumin). Psoriasis area severity index (PASI) score, ear/back skin thickness, body weight alterations, and histopathological examination were employed to analyze disease severity. The spleen index studied the systemic effect. Strain effect on oxidative stress induced by IMQ was evaluated by estimating antioxidant factors, superoxide dismutase (SOD), catalase, and glutathione (GSH). RESULTS IMQ application resulted in increased PASI score, thickness, and alterations in body weight, confirming disease development in all the mice. However, the disease stability/severity between these strains was not identical. Although IMQ application caused splenomegaly, IMQ+curcumin treated C57BL/6 mice demonstrated a synergistic effect of IMQ and curcumin on the spleen resulting in increased splenomegaly. Decreased cellular enzyme activity in SOD, Catalase, and levels of GSH was observed in IMQ challenged mice, indicating the participation of the redox system in the genesis of the disease that was comparable among the strains. CONCLUSIONS These results indicate the existence of strain-dependent development of the disease. The Swiss model was found to be better in terms of disease severity and stability than other models. Further, a detailed mechanistic study might help to explain the pathological difference between these strains.
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Affiliation(s)
- Murali Badanthadka
- Department of Nitte University Centre for Animal Research and Experimentation (NUCARE), NGSM Institute of Pharmaceutical Sciences (NGSMIPS), NITTE (Deemed to be University), Paneer, Deralakatte, Mangalore, 575 018, India
| | - Lidwin D'Souza
- Department of Pharmacovigilance, Norwich Clinical Services, Bangalore, India
| | - Fathima Salwa
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences, Mangalore, India
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