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Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Brain 2024; 147:1553-1570. [PMID: 38128548 PMCID: PMC10994532 DOI: 10.1093/brain/awad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.
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Affiliation(s)
- Amrita K Singh
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Stephen Viviano
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaojie Ma
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Shujuan Zhao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John P Shohfi
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, UK
| | - Syed R A Rizvi
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Seth L Alper
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nenad Sestan
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Hermela Shimelis
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lauren K Walsh
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
- Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Sheng Chih Jin
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | - Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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2
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. medRxiv 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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Kundishora AJ, Allington G, McGee S, Mekbib KY, Gainullin V, Timberlake AT, Nelson-Williams C, Kiziltug E, Smith H, Ocken J, Shohfi J, Allocco A, Duy PQ, Elsamadicy AA, Dong W, Zhao S, Wang YC, Qureshi HM, DiLuna ML, Mane S, Tikhonova IR, Fu PY, Castaldi C, López-Giráldez F, Knight JR, Furey CG, Carter BS, Haider S, Moreno-De-Luca A, Alper SL, Gunel M, Millan F, Lifton RP, Torene RI, Jin SC, Kahle KT. Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts. Nat Med 2023; 29:667-678. [PMID: 36879130 DOI: 10.1038/s41591-023-02238-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/26/2023] [Indexed: 03/08/2023]
Abstract
Cerebral arachnoid cysts (ACs) are one of the most common and poorly understood types of developmental brain lesion. To begin to elucidate AC pathogenesis, we performed an integrated analysis of 617 patient-parent (trio) exomes, 152,898 human brain and mouse meningeal single-cell RNA sequencing transcriptomes and natural language processing data of patient medical records. We found that damaging de novo variants (DNVs) were highly enriched in patients with ACs compared with healthy individuals (P = 1.57 × 10-33). Seven genes harbored an exome-wide significant DNV burden. AC-associated genes were enriched for chromatin modifiers and converged in midgestational transcription networks essential for neural and meningeal development. Unsupervised clustering of patient phenotypes identified four AC subtypes and clinical severity correlated with the presence of a damaging DNV. These data provide insights into the coordinated regulation of brain and meningeal development and implicate epigenomic dysregulation due to DNVs in AC pathogenesis. Our results provide a preliminary indication that, in the appropriate clinical context, ACs may be considered radiographic harbingers of neurodevelopmental pathology warranting genetic testing and neurobehavioral follow-up. These data highlight the utility of a systems-level, multiomics approach to elucidate sporadic structural brain disease.
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Affiliation(s)
- Adam J Kundishora
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Garrett Allington
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | | | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Jack Ocken
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - John Shohfi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Aladine A Elsamadicy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Weilai Dong
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Shujuan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yung-Chun Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hanya M Qureshi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Shrikant Mane
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Yale Center for Genomic Analysis, Yale University, West Haven, CT, USA
| | | | - Po-Ying Fu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | - James R Knight
- Yale Center for Genomic Analysis, Yale University, West Haven, CT, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Shozeb Haider
- School of Pharmacy, University College London, London, UK
| | - Andres Moreno-De-Luca
- Department of Radiology, Autism and Developmental Medicine Institute, Genomic Medicine Institute, Geisinger, Danville, PA, USA
| | - Seth L Alper
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Murat Gunel
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | | | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | | | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Timberlake AT, Kiziltug E, Jin SC, Nelson-Williams C, Loring E, Allocco A, Marlier A, Banka S, Stuart H, Passos-Buenos MR, Rosa R, Rogatto SR, Tonne E, Stiegler AL, Boggon TJ, Alperovich M, Steinbacher D, Staffenberg DA, Flores RL, Persing JA, Kahle KT, Lifton RP. De novo mutations in the BMP signaling pathway in lambdoid craniosynostosis. Hum Genet 2023; 142:21-32. [PMID: 35997807 DOI: 10.1007/s00439-022-02477-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023]
Abstract
Lambdoid craniosynostosis (CS) is a congenital anomaly resulting from premature fusion of the cranial suture between the parietal and occipital bones. Predominantly sporadic, it is the rarest form of CS and its genetic etiology is largely unexplored. Exome sequencing of 25 kindreds, including 18 parent-offspring trios with sporadic lambdoid CS, revealed a marked excess of damaging (predominantly missense) de novo mutations that account for ~ 40% of sporadic cases. These mutations clustered in the BMP signaling cascade (P = 1.6 × 10-7), including mutations in genes encoding BMP receptors (ACVRL1 and ACVR2A), transcription factors (SOX11, FOXO1) and a transcriptional co-repressor (IFRD1), none of which have been implicated in other forms of CS. These missense mutations are at residues critical for substrate or target sequence recognition and many are inferred to cause genetic gain-of-function. Additionally, mutations in transcription factor NFIX were implicated in syndromic craniosynostosis affecting diverse sutures. Single cell RNA sequencing analysis of the mouse lambdoid suture identified enrichment of mutations in osteoblast precursors (P = 1.6 × 10-6), implicating perturbations in the balance between proliferation and differentiation of osteoprogenitor cells in lambdoid CS. The results contribute to the growing knowledge of the genetics of CS, have implications for genetic counseling, and further elucidate the molecular etiology of premature suture fusion.
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Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA.
| | - Emre Kiziltug
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | | | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helen Stuart
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | | | - Rafael Rosa
- Clinical Genetics, UFCSPA and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Silvia R Rogatto
- Neogene Laboratory, Research Center (CIPE), AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - Elin Tonne
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Michael Alperovich
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Derek Steinbacher
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - David A Staffenberg
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Roberto L Flores
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. .,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.
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5
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Dong W, Jin SC, Allocco A, Zeng X, Sheth AH, Panchagnula S, Castonguay A, Lorenzo LÉ, Islam B, Brindle G, Bachand K, Hu J, Sularz A, Gaillard J, Choi J, Dunbar A, Nelson-Williams C, Kiziltug E, Furey CG, Conine S, Duy PQ, Kundishora AJ, Loring E, Li B, Lu Q, Zhou G, Liu W, Li X, Sierant MC, Mane S, Castaldi C, López-Giráldez F, Knight JR, Sekula RF, Simard JM, Eskandar EN, Gottschalk C, Moliterno J, Günel M, Gerrard JL, Dib-Hajj S, Waxman SG, Barker FG, Alper SL, Chahine M, Haider S, De Koninck Y, Lifton RP, Kahle KT. Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia. iScience 2020; 23:101552. [PMID: 33083721 PMCID: PMC7554653 DOI: 10.1016/j.isci.2020.101552] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
Trigeminal neuralgia (TN) is a common, debilitating neuropathic face pain syndrome often resistant to therapy. The familial clustering of TN cases suggests that genetic factors play a role in disease pathogenesis. However, no unbiased, large-scale genomic study of TN has been performed to date. Analysis of 290 whole exome-sequenced TN probands, including 20 multiplex kindreds and 70 parent-offspring trios, revealed enrichment of rare, damaging variants in GABA receptor-binding genes in cases. Mice engineered with a TN-associated de novo mutation (p.Cys188Trp) in the GABAA receptor Cl− channel γ-1 subunit (GABRG1) exhibited trigeminal mechanical allodynia and face pain behavior. Other TN probands harbored rare damaging variants in Na+ and Ca+ channels, including a significant variant burden in the α-1H subunit of the voltage-gated Ca2+ channel Cav3.2 (CACNA1H). These results provide exome-level insight into TN and implicate genetically encoded impairment of GABA signaling and neuronal ion transport in TN pathogenesis. Genomic analysis of trigeminal neuralgia (TN) using exome sequencing Rare mutations in GABA signaling and ion transport genes are enriched in TN cases Generation of a genetic TN mouse model engineered with a patient-specific mutation
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Affiliation(s)
- Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - August Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Xue Zeng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Amar H Sheth
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Annie Castonguay
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada
| | | | - Barira Islam
- University College London, School of Pharmacy, London, England
| | | | - Karine Bachand
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada
| | - Jamie Hu
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Agata Sularz
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan Gaillard
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.,Department of Biomedical Sciences, Korea University College of Medicine, 02841 Seoul, Korea
| | - Ashley Dunbar
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Sierra Conine
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Adam J Kundishora
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Erin Loring
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Geyu Zhou
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Wei Liu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Xinyue Li
- School of Data Science, City University of Hong Kong, Hong Kong, China
| | - Michael C Sierant
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, West Haven, CT, USA
| | | | | | | | - Raymond F Sekula
- Department of Neurological Surgery, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - J Marc Simard
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emad N Eskandar
- Department of Neurological Surgery, Albert Einstein College of Medicine, Montefiore Medical Center, New York
| | | | | | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jason L Gerrard
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Sulayman Dib-Hajj
- Center for Neuroscience & Regeneration Research, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Neurology; Yale University, New Haven, CT, USA
| | - Stephen G Waxman
- Center for Neuroscience & Regeneration Research, VA Connecticut Healthcare System, West Haven, CT, USA.,Department of Neurology; Yale University, New Haven, CT, USA
| | - Fred G Barker
- Harvard Medical School, Boston, MA, USA.,Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mohamed Chahine
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada.,Department of Medicine, Université Laval, Québec, QC, Canada
| | - Shozeb Haider
- University College London, School of Pharmacy, London, England
| | - Yves De Koninck
- CERVO Brain Research Centre, Université Laval, Québec, QC, Canada.,Department of Psychiatry and Neuroscience, Université Laval, Québec, QC, Canada
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.,Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
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6
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Fomchenko EI, Erson-Omay EZ, Kundishora AJ, Hong CS, Daniel AA, Allocco A, Duy PQ, Darbinyan A, Marks AM, DiLuna ML, Kahle KT, Huttner A. Genomic alterations underlying spinal metastases in pediatric H3K27M-mutant pineal parenchymal tumor of intermediate differentiation: case report. J Neurosurg Pediatr 2019; 25:121-130. [PMID: 31653819 DOI: 10.3171/2019.8.peds18664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 08/21/2019] [Indexed: 11/06/2022]
Abstract
Pediatric midline tumors are devastating high-grade lesions with a dismal prognosis and no curative surgical options. Here, the authors report the clinical presentation, surgical management, whole-exome sequencing (WES), and clonality analysis of a patient with a radically resected H3K27M-mutant pineal parenchymal tumor (PPT) and spine metastases consistent with PPT of intermediate differentiation (PPTID). They identified somatic mutations in H3F3A (H3K27M), FGFR1, and NF1 both in the original PPT and in the PPTID metastases. They also found 12q amplification containing CDK4/MDM2 and chromosome 17 loss of heterozygosity overlapping with NF1 that resulted in biallelic NF1 loss. They noted a hypermutated phenotype with increased C>T transitions within the PPTID metastases and 2p amplification overlapping with the MYCN locus. Clonality analysis detected three founder clones maintained during progression and metastasis. Tumor clones present within the PPTID metastases but not the pineal midline tumor harbored mutations in APC and TIMP2.While the majority of H3K27M mutations are found in pediatric midline gliomas, it is increasingly recognized that this mutation is present in a wider range of lesions with a varied morphological appearance. The present case appears to be the first description of H3K27M mutation in PPTID. Somatic mutations in H3F3A, FGFR1, and NF1 have been suggested to be driver mutations in pediatric midline gliomas. Their clonality and presence in over 80% of tumor cells in our patient's PPTID are consistent with similarly crucial roles in early tumorigenesis, with progression mediated by copy number variations and chromosomal aberrations involving known oncogenes and tumor suppressors. The roles of APC and TIMP2 mutations in progression and metastasis remain to be investigated.
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Affiliation(s)
| | | | | | | | - Ava A Daniel
- 8Yale College, Yale University, New Haven, Connecticut
| | | | | | | | | | | | - Kristopher T Kahle
- Departments of1Neurosurgery
- 4Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine; and
- 5Pediatrics
- 6Cellular & Molecular Physiology, and
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7
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Jin SC, Furey CG, Zeng X, Allocco A, Nelson‐Williams C, Dong W, Karimy JK, Wang K, Ma S, Delpire E, Kahle KT. SLC12A ion transporter mutations in sporadic and familial human congenital hydrocephalus. Mol Genet Genomic Med 2019; 7:e892. [PMID: 31393094 PMCID: PMC6732308 DOI: 10.1002/mgg3.892] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/15/2019] [Accepted: 07/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Congenital hydrocephalus (CH) is a highly morbid disease that features enlarged brain ventricles and impaired cerebrospinal fluid homeostasis. Although early linkage or targeted sequencing studies in large multigenerational families have localized several genes for CH, the etiology of most CH cases remains unclear. Recent advances in whole exome sequencing (WES) have identified five new bona fide CH genes, implicating impaired regulation of neural stem cell fate in CH pathogenesis. Nonetheless, in the majority of CH cases, the pathological etiology remains unknown, suggesting more genes await discovery. METHODS WES of family members of a sporadic and familial form of severe L1CAM mutation-negative CH associated with aqueductal stenosis was performed. Rare genetic variants were analyzed, prioritized, and validated. De novo copy number variants (CNVs) were identified using the XHMM algorithm and validated using qPCR. Xenopus oocyte experiments were performed to access mutation impact on protein function and expression. RESULTS A novel inherited protein-damaging mutation (p.Pro605Leu) in SLC12A6, encoding the K+ -Cl- cotransporter KCC3, was identified in both affected members of multiplex kindred CHYD110. p.Pro605 is conserved in KCC3 orthologs and among all human KCC paralogs. The p.Pro605Leu mutation maps to the ion-transporting domain, and significantly reduces KCC3-dependent K+ transport. A novel de novo CNV (deletion) was identified in SLC12A7, encoding the KCC3 paralog and binding partner KCC4, in another family (CHYD130) with sporadic CH. CONCLUSION These findings identify two novel, related genes associated with CH, and implicate genetically encoded impairments in ion transport for the first time in CH pathogenesis.
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Affiliation(s)
- Sheng Chih Jin
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Laboratory of Human Genetics and GenomicsThe Rockefeller UniversityNew YorkNYUSA
| | - Charuta G. Furey
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Department of NeurosurgeryYale University School of MedicineNew HavenCTUSA
| | - Xue Zeng
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - August Allocco
- Department of NeurosurgeryYale University School of MedicineNew HavenCTUSA
| | | | - Weilai Dong
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - Jason K. Karimy
- Department of NeurosurgeryYale University School of MedicineNew HavenCTUSA
| | - Kevin Wang
- Department of NeurosurgeryYale University School of MedicineNew HavenCTUSA
| | - Shaojie Ma
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
| | - Eric Delpire
- Department of AnesthesiologyVanderbilt University School of MedicineNashvilleTNUSA
| | - Kristopher T. Kahle
- Department of GeneticsYale University School of MedicineNew HavenCTUSA
- Department of NeurosurgeryYale University School of MedicineNew HavenCTUSA
- Department of Cellular & Molecular PhysiologyYale University School of MedicineNew HavenCTUSA
- NIH‐Yale Centers for Mendelian Genomics, Yale School of MedicineNew HavenCTUSA
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8
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Duran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, Kahle KT. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation. Neuron 2019; 101:429-443.e4. [PMID: 30578106 DOI: 10.1016/j.neuron.2018.11.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/12/2018] [Accepted: 11/20/2018] [Indexed: 02/05/2023]
Abstract
Normal vascular development includes the formation and specification of arteries, veins, and intervening capillaries. Vein of Galen malformations (VOGMs) are among the most common and severe neonatal brain arterio-venous malformations, shunting arterial blood into the brain's deep venous system through aberrant direct connections. Exome sequencing of 55 VOGM probands, including 52 parent-offspring trios, revealed enrichment of rare damaging de novo mutations in chromatin modifier genes that play essential roles in brain and vascular development. Other VOGM probands harbored rare inherited damaging mutations in Ephrin signaling genes, including a genome-wide significant mutation burden in EPHB4. Inherited mutations showed incomplete penetrance and variable expressivity, with mutation carriers often exhibiting cutaneous vascular abnormalities, suggesting a two-hit mechanism. The identified mutations collectively account for ∼30% of studied VOGM cases. These findings provide insight into disease biology and may have clinical implications for risk assessment.
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Affiliation(s)
- Daniel Duran
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Xue Zeng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | | | - Bogdan Yatsula
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Jonathan Gaillard
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Michelle A Sorscher
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Loring
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer Klein
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA
| | - August Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Ava Hunt
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Sierra Conine
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Jason K Karimy
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Mark W Youngblood
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratory, Exeter, UK
| | - Michael L DiLuna
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Charles C Matouk
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, West Haven, CT, USA
| | | | | | | | - James Knight
- Yale Center for Genome Analysis, West Haven, CT, USA
| | - Shozeb Haider
- University College London, School of Pharmacy, London, UK
| | - Mariya Soban
- University College London, School of Pharmacy, London, UK; Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Masaki Komiyama
- Department of Neurointervention, Osaka City General Hospital, Osaka, Japan
| | - Andrew F Ducruet
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Joseph M Zabramski
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Alan Dardik
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Brian P Walcott
- Department of Neurological Surgery, University of Southern California, Los Angeles, CA, USA
| | - Christopher J Stapleton
- Department of Neurological Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Georges Rodesch
- Service de Neuroradiologie Diagnostique et Thérapeutique, Hôpital Foch, Suresnes, France
| | - Eric Jackson
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Edward R Smith
- Department of Neurointerventional Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Darren B Orbach
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA; Department of Neurointerventional Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Alejandro Berenstein
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kaya Bilguvar
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Yale Center for Genome Analysis, West Haven, CT, USA
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA; Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA; Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA.
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9
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Fomchenko EI, Duran D, Jin SC, Dong W, Erson-Omay EZ, Antwi P, Allocco A, Gaillard JR, Huttner A, Gunel M, DiLuna ML, Kahle KT. De novo MYH9 mutation in congenital scalp hemangioma. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002998. [PMID: 29903892 PMCID: PMC6071566 DOI: 10.1101/mcs.a002998] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/19/2022] Open
Abstract
Congenital hemangiomas are tumor-like vascular malformations with poorly understood pathogenesis. We report the case of a neonate with a massive congenital scalp hemangioma that required urgent neurosurgical removal on the second day of life because of concern for high-flow arteriovenous shunting. Exome sequencing identified a rare damaging de novo germline mutation in MYH9 (c.5308C>T, p.[Arg1770Cys]), encoding the MYH9 nonmuscle myosin IIA. MYH9 has a probability of loss-of-function intolerance (pLI) score of >0.99 and is highly intolerant to missense variation (z score = 5.59). The p.(Arg1770Cys) mutation substitutes an evolutionarily conserved amino acid in the protein's critical myosin tail domain and is predicted to be highly deleterious by SIFT, PolyPhen-2, MetaSVM, and CADD. MYH9 is a known regulator of cytokinesis, VEGF-regulated angiogenesis, and p53-dependent tumorigenesis. These findings reveal a novel association of germline de novo MYH9 mutation with congenital hemangioma.
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Affiliation(s)
- Elena I Fomchenko
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Weilai Dong
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - E Zeynep Erson-Omay
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - August Allocco
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Jonathan R Gaillard
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Murat Gunel
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06519, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Centers for Mendelian Genomics and Yale Program on Neurogenetics, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut 06519, USA.,Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06519, USA
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10
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Furey CG, Choi J, Jin SC, Zeng X, Timberlake AT, Nelson-Williams C, Mansuri MS, Lu Q, Duran D, Panchagnula S, Allocco A, Karimy JK, Khanna A, Gaillard JR, DeSpenza T, Antwi P, Loring E, Butler WE, Smith ER, Warf BC, Strahle JM, Limbrick DD, Storm PB, Heuer G, Jackson EM, Iskandar BJ, Johnston JM, Tikhonova I, Castaldi C, López-Giráldez F, Bjornson RD, Knight JR, Bilguvar K, Mane S, Alper SL, Haider S, Guclu B, Bayri Y, Sahin Y, Apuzzo MLJ, Duncan CC, DiLuna ML, Günel M, Lifton RP, Kahle KT. De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. Neuron 2018; 99:302-314.e4. [PMID: 29983323 DOI: 10.1016/j.neuron.2018.06.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/03/2018] [Accepted: 06/12/2018] [Indexed: 12/30/2022]
Abstract
Congenital hydrocephalus (CH), featuring markedly enlarged brain ventricles, is thought to arise from failed cerebrospinal fluid (CSF) homeostasis and is treated with lifelong surgical CSF shunting with substantial morbidity. CH pathogenesis is poorly understood. Exome sequencing of 125 CH trios and 52 additional probands identified three genes with significant burden of rare damaging de novo or transmitted mutations: TRIM71 (p = 2.15 × 10-7), SMARCC1 (p = 8.15 × 10-10), and PTCH1 (p = 1.06 × 10-6). Additionally, two de novo duplications were identified at the SHH locus, encoding the PTCH1 ligand (p = 1.2 × 10-4). Together, these probands account for ∼10% of studied cases. Strikingly, all four genes are required for neural tube development and regulate ventricular zone neural stem cell fate. These results implicate impaired neurogenesis (rather than active CSF accumulation) in the pathogenesis of a subset of CH patients, with potential diagnostic, prognostic, and therapeutic ramifications.
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Affiliation(s)
- Charuta Gavankar Furey
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Carol Nelson-Williams
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - M Shahid Mansuri
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Duran
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shreyas Panchagnula
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jason K Karimy
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Arjun Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan R Gaillard
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Prince Antwi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - William E Butler
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Edward R Smith
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer M Strahle
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - David D Limbrick
- Department of Neurological Surgery and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Phillip B Storm
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gregory Heuer
- Department of Neurosurgery, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Bermans J Iskandar
- Department of Neurological Surgery, University of Wisconsin Medical School, Madison, WI 53726, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama School of Medicine, Birmingham, AL 35233, USA
| | - Irina Tikhonova
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | | | | | - Robert D Bjornson
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - James R Knight
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Kaya Bilguvar
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Shrikant Mane
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Seth L Alper
- Division of Nephrology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, UK
| | - Bulent Guclu
- Kartal Dr. Lutfi Kirdar Research and Training Hospital, Istanbul 34860, Turkey
| | - Yasar Bayri
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Yener Sahin
- Acibadem Mehmet Ali Aydinlar University, School of Medicine, Department of Neurosurgery, Division of Pediatric Neurosurgery, Istanbul 34752, Turkey
| | - Michael L J Apuzzo
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles C Duncan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Murat Günel
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Kristopher T Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06510, USA.
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Cuffini AM, Tullio V, Bonino A, Allocco A, Palarchio AI, Carlone NA. Entry of sanfetrinem into human polymorphonuclear granulocytes and its cell-associated activity against intracellular, penicillin-resistant Streptococcus pneumoniae. Antimicrob Agents Chemother 1998; 42:1745-50. [PMID: 9661015 PMCID: PMC105677 DOI: 10.1128/aac.42.7.1745] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/1997] [Accepted: 04/27/1998] [Indexed: 02/08/2023] Open
Abstract
The entry of antibiotics into phagocytes is necessary for activity against intracellular pathogens. The ability of sanfetrinem, the first member of a new class of antibiotics, to penetrate human polymorphonuclear granulocytes and its consequences upon subsequent phagocytosis and killing of ingested penicillin-resistant Streptococcus pneumoniae have been evaluated. Sanfetrinem penetrated into human polymorphonuclear leukocytes (PMNs) at all concentrations tested, with cellular concentration/extracellular concentration ratios of 6.6 to 5.03 and 4.21 when sanfetrinem was used at 0.25 to 0.5 and 1 microgram/ml, respectively, within 30 min of incubation. The uptake was complete within 5 min and was not energy dependent, since it was not affected by cell viability, environmental temperature, or the addition of a metabolic inhibitor. At a concentration of one-half the MIC, sanfetrinem significantly enhanced human PMN phagocytosis and increased intracellular bactericidal activity against penicillin-resistant S. pneumoniae. Following preexposure of PMNs to a concentration of one-half the MIC of sanfetrinem, there was a significant increase in both phagocytosis and killing compared with that for the controls, indicating the ability of sanfetrinem to interact with biological membranes and remain active within PMNs. Preexposure of streptococci to sanfetrinem made penicillin-resistant S. pneumoniae more susceptible to the bactericidal mechanisms of human PMNs than untreated organisms.
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Affiliation(s)
- A M Cuffini
- Department of Public Health and Microbiology, University of Turin, Italy.
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Cuffini AM, Tullio V, Allocco A, Paizis G, De Leo C, Carlone NA. Effect of rufloxacin upon non-specific immune defences: in-vitro, ex-vivo and in-vivo results. J Antimicrob Chemother 1994; 34:545-53. [PMID: 7868406 DOI: 10.1093/jac/34.4.545] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
This study investigated in-vitro, ex-vivo and in-vivo the immunomodulatory effects of rufloxacin. 0.5 MIC of rufloxacin significantly enhanced human macrophage phagocytosis and increased intracellular killing of Klebsiella pneumoniae in vitro. Pre-incubation of K. pneumoniae with rufloxacin made the bacteria more susceptible to both phagocytosis and intracellular killing by human macrophages than control organisms. Following pre-exposure of macrophages to 0.5 MIC of rufloxacin, there was a significant increase in the intracellular killing of K. pneumoniae compared with the controls, indicating the ability of rufloxacin to cross biological membranes and to remain active within phagocytes. Ex-vivo experiments show that iv administration of rufloxacin in mice lead to an increase in both phagocytic and microbicidal intracellular activity by phagocytes. In-vivo models of experimental infections showed that prophylactic administration of rufloxacin increased the survival of mice after challenge with Candida albicans.
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Affiliation(s)
- A M Cuffini
- Institute of Microbiology, University of Turin, Italy
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Tullio V, Cuffini AM, Cavallo R, Allocco A, Carlone NA. Effect of ceftriaxone on the phagocytosis and intracellular killing of Staphylococcus aureus by human macrophages. J Chemother 1994; 6:177-83. [PMID: 7983500 DOI: 10.1080/1120009x.1994.11741149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The efficacy of an antimicrobial agent in the treatment of infections depends upon the interactions of bacteria, antibiotic and phagocytes. The influence of ceftriaxone on the phagocytic and bactericidal activity of human macrophages in vitro and ex vivo was investigated. At concentrations one-half the minimum inhibitory concentration (1/2 x MIC) the antibiotic caused in vitro a significant enhancement of phagocytosis and a reduction in the survival of intracellular Staphylococcus aureus. The distinction between any effect of ceftriaxone on the staphylococci and the macrophages was made by exposure of each of them to the antibiotic before they were incubated together. The results suggest that ceftriaxone may have a direct positive action on macrophages, possibly by interfering with the cellular membrane functions and hence enhancing engulfment of bacteria. The ex vivo data seem to corroborate this hypothesis.
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Affiliation(s)
- V Tullio
- Institute of Microbiology, University of Turin, Italy
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Allocco A, Tullio V, Cuffini AM, Carlone NA. [In vitro activity of several antibiotics on pathogenic micro-organisms isolated from the lower respiratory tract]. G Batteriol Virol Immunol 1994; 86:15-28. [PMID: 8706972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Lower respiratory tract infections are clinically important, because of their high incidence, as well as the significant morbidity they cause. Hence the great importance to diagnose the etiology of these infections and treat the patient with selective therapy. In this study 367 bacteria isolated from lower respiratory tract were identified (253 Gram negative and 114 Gram positive) and tested towards augmentin, ceftriaxone, lomefloxacin, ciprofloxacin, ofloxacin and erythromycin. The in vitro activity of such antibiotics against the clinical isolates was compared.
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Affiliation(s)
- A Allocco
- Istituto di Microbiologia, Università degli studi di Torino
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Cuffini AM, Tullio V, Allocco A, Giachino F, Fazari S, Carlone NA. The entry of meropenem into human macrophages and its immunomodulating activity. J Antimicrob Chemother 1993; 32:695-703. [PMID: 8125834 DOI: 10.1093/jac/32.5.695] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The uptake of meropenem by human macrophages and its consequences upon subsequent phagocytosis and killing of intracellular staphylococci has been studied. The cellular to extracellular concentration ratios (C/E) of meropenem were always high (range 3-12) at extracellular concentrations ranging from 0.125 to 1 mg/L. The uptake was not energy-dependent, being similar when viable and formalin-killed cells were used and was influenced neither by environmental temperature nor by the addition of a metabolic inhibitor. Meropenem at half the MIC caused a significant enhancement of phagocytosis and a reduction in the survival of intracellular Staphylococcus aureus. Pre-exposure of either staphylococci or macrophages to sub-MIC concentrations of meropenem led to an increase in uptake of bacteria and intracellular bactericidal activity by macrophages.
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Affiliation(s)
- A M Cuffini
- Institute of Microbiology, University of Turin, Torino, Italy
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Cuffini AM, Tullio V, Allocco A, Fazari S, Giachino F, Carlone NA. Enhanced Staphylococcus aureus susceptibility to immunodefences induced by sub-inhibitory and bactericidal concentrations of imipenem. J Antimicrob Chemother 1993; 31:559-68. [PMID: 8514650 DOI: 10.1093/jac/31.4.559] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Recent evidence suggests that the selection of an antibiotic for the treatment of infection should take into account not only the drug's antimicrobial activity but also the way in which it interacts with host defence mechanisms, since this may influence the response to infection. In this study we have investigated the effects of imipenem on the activities of human macrophages against Staphylococcus aureus. Bacterial susceptibility to phagocytosis and intracellular killing were determined after S. aureus and macrophages were incubated both simultaneously with sub-inhibitory and bactericidal concentrations of imipenem and following pre-exposure of the organisms and the macrophages individually to the same concentrations of imipenem. At both concentrations and under both circumstances, imipenem potentiated the phagocytic and microbicidal activities of the macrophages.
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Affiliation(s)
- A M Cuffini
- Institute of Microbiology, University of Turin, Torino, Italy
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Allocco A, Giachino F, Tuninetti L, Tullio V, Cuffini AM, Carlone NA. [Urinary infection. II. Comparative in vitro activities of several antibiotic drugs against Gram-positive bacteria]. G Batteriol Virol Immunol 1992; 85:68-78. [PMID: 7498618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this study the in vitro susceptibility of 1,009 Gram-positive strains isolated from 4,505 positive urocultures was evaluated towards the following chemotherapeutic agents: oxacillin, ampicillin, amoxicillin + clavulanic acid, imipenem, cefalotin, cefotaxime, amikacin, gentamicin, ciprofloxacin, pefloxacin, clindamycin, erythromycin, vancomycin, rifampicin, tetracycline and chloramphenicol. The results indicate that vancomycin is the most active antibiotic against all the strains, including enterococci often involved in serious infections caused by invasive techniques.
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Affiliation(s)
- A Allocco
- Istituto di Microbiologia, Università di Torino
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Giachino F, Allocco A, Tuninetti L, Tullio V, Cuffini AM, Carlone NA. [Urinary infection. I. Comparative in vitro activities of several antibiotic drugs against Gram-negative bacteria]. G Batteriol Virol Immunol 1992; 85:55-67. [PMID: 7498617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The in vitro activity of imipenem against 3,496 Gram-negative strains isolated from 4,505 positive urocultures was determined. The effectiveness of imipenem was then compared with that of ampicillin, amoxycillin + clavulanic acid, ticarcillin, piperacillin, aztreonam, cefalotin , ceftazidime, cefoxitin, cefotaxime, norfloxacin, ciprofloxacin, amikacin, gentamicin, tobramycin, trimethoprim + sulfamethoxazole. Imipenem was active against all isolates, including Pseudomonas spp. known to account for a large portion of nosocomial infections and resistance to antibacterial drugs.
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Affiliation(s)
- F Giachino
- Istituto di Microbiologia, Università di Torino
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