1
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Ressler AK, Snellings DA, Girard R, Gallione CJ, Lightle R, Allen AS, Awad IA, Marchuk DA. Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations. Nat Commun 2023; 14:7009. [PMID: 37919320 PMCID: PMC10622526 DOI: 10.1038/s41467-023-42908-w] [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: 04/21/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023] Open
Abstract
Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, including a somatic, activating mutation in the oncogene PIK3CA, as well as biallelic loss-of-function mutations in a CCM gene. However, standard sequencing approaches often fail to yield a full complement of pathogenic mutations in many CCMs. We suggest this reality reflects the limited sensitivity to identify low-frequency variants and the presence of mutations undetectable with bulk short-read sequencing. Here we report a single-nucleus DNA-sequencing approach that leverages the underlying biology of CCMs to identify lesions with somatic loss-of-heterozygosity, a class of such hidden mutations. We identify an alternative genetic mechanism for CCM pathogenesis and establish a method that can be repurposed to investigate the genetic underpinning of other disorders with multiple somatic mutations.
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Affiliation(s)
- Andrew K Ressler
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Carol J Gallione
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27710, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA.
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2
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Au EH, Fauci C, Luo Y, Mangan RJ, Snellings DA, Shoben CR, Weaver S, Simpson SK, Lowe CB. Gonomics: uniting high performance and readability for genomics with Go. Bioinformatics 2023; 39:btad516. [PMID: 37624924 PMCID: PMC10466080 DOI: 10.1093/bioinformatics/btad516] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/19/2023] [Accepted: 08/24/2023] [Indexed: 08/27/2023] Open
Abstract
SUMMARY Many existing software libraries for genomics require researchers to pick between competing considerations: the performance of compiled languages and the accessibility of interpreted languages. Go, a modern compiled language, provides an opportunity to address this conflict. We introduce Gonomics, an open-source collection of command line programs and bioinformatic libraries implemented in Go that unites readability and performance for genomic analyses. Gonomics contains packages to read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, and VCF), and can convert and interface between these formats. Furthermore, our modular library structure provides a flexible platform for researchers developing their own software tools to address specific questions. These commands can be combined and incorporated into complex pipelines to meet the growing need for high-performance bioinformatic resources. AVAILABILITY AND IMPLEMENTATION Gonomics is implemented in the Go programming language. Source code, installation instructions, and documentation are freely available at https://github.com/vertgenlab/gonomics.
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Affiliation(s)
- Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Christiana Fauci
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States
| | - Yanting Luo
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States
| | - Riley J Mangan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Chelsea R Shoben
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States
| | - Seth Weaver
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States
| | - Shae K Simpson
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, United States
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, United States
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3
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Mangan RJ, Alsina FC, Mosti F, Sotelo-Fonseca JE, Snellings DA, Au EH, Carvalho J, Sathyan L, Johnson GD, Reddy TE, Silver DL, Lowe CB. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell 2022; 185:4587-4603.e23. [PMID: 36423581 PMCID: PMC10013929 DOI: 10.1016/j.cell.2022.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/14/2022] [Indexed: 11/24/2022]
Abstract
Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.
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Affiliation(s)
- Riley J Mangan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Fernando C Alsina
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Eric H Au
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Juliana Carvalho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Laya Sathyan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Graham D Johnson
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy E Reddy
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA; Departments of Cell Biology and Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27705, USA.
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4
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Galeffi F, Snellings DA, Wetzel-Strong SE, Kastelic N, Bullock J, Gallione CJ, North PE, Marchuk DA. A novel somatic mutation in GNAQ in a capillary malformation provides insight into molecular pathogenesis. Angiogenesis 2022; 25:493-502. [PMID: 35635655 DOI: 10.1007/s10456-022-09841-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/13/2022] [Accepted: 05/09/2022] [Indexed: 01/01/2023]
Abstract
Sturge-Weber syndrome (SWS) is a sporadic, congenital, neuro-cutaneous disorder characterized by a mosaic, capillary malformation. SWS and non-syndromic capillary malformations are both caused by a somatic activating mutation in GNAQ encoding the G protein subunit alpha-q protein. The missense mutation R183Q is the sole GNAQ mutation identified thus far in 90% of SWS-associated or isolated capillary malformations. In this study, we sequenced skin biopsies of capillary malformations from 9 patients. We identified the R183Q mutation in nearly all samples, but one sample exhibited a Q209R mutation. This new mutation occurs at the same residue as the constitutively-activating Q209L mutation, commonly seen in tumors. However, Q209R is a rare variant in this gene. To compare the effect of the Q209R mutation on downstream signaling, we performed reporter assays with a GNAQ-responsive reporter co-transfected with either GNAQ WT, R183Q, Q209L, Q209R, or C9X (representing a null allele). Q209L showed the highest reporter activation, with R183Q and Q209R showing significantly lower activation. To determine whether these mutations had similar or different downstream consequences we performed RNA-seq analysis in microvascular endothelial cells (HMEC-1) electroporated with the same GNAQ variants. The R183 and Q209 missense variants caused extensive dysregulation of a broad range of transcripts compared to the WT or null allele, confirming that these are all activating mutations. However, the missense variants exhibited very few differentially expressed genes (DEGs) when compared to each other. These data suggest that these activating GNAQ mutations differ in magnitude of activation but have similar downstream effects.
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Affiliation(s)
- F Galeffi
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - D A Snellings
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - S E Wetzel-Strong
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - N Kastelic
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - J Bullock
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - C J Gallione
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - P E North
- Medical College of Wisconsin, Milwaukee, WI, USA
| | - D A Marchuk
- Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA.
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5
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Snellings DA, Girard R, Lightle R, Srinath A, Romanos S, Li Y, Chen C, Ren AA, Kahn ML, Awad IA, Marchuk DA. Developmental venous anomalies are a genetic primer for cerebral cavernous malformations. Nat Cardiovasc Res 2022; 1:246-252. [PMID: 35355835 PMCID: PMC8958845 DOI: 10.1038/s44161-022-00035-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/04/2022] [Indexed: 01/22/2023]
Abstract
Cerebral cavernous malformations (CCM) are a neurovascular anomaly that may occur sporadically, or be inherited due to autosomal dominant mutations in KRIT1 , CCM2 , or PDCD10 . Individual lesions are caused by somatic mutations which have been identified in KRIT1, CCM2, PDCD10, MAP3K3, and PIK3CA . However, the interactions between mutations, and their relative contributions to sporadic versus familial cases remain unclear. We show that mutations in KRIT1, CCM2, PDCD10, and MAP3K3 are mutually exclusive, but may co-occur with mutations in PIK3CA. We also find that MAP3K3 mutations may cause sporadic, but not familial CCM. Furthermore, we find identical PIK3CA mutations in CCMs and adjacent developmental venous anomalies (DVA), a common vascular malformation frequently found in the vicinity of sporadic CCMs. However, somatic mutations in MAP3K3 are found only in the CCM. This suggests that sporadic CCMs are derived from cells of the DVA which have acquired an additional mutation in MAP3K3 .
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Affiliation(s)
- Daniel A. Snellings
- Department of Molecular Genetics and Microbiology, Duke
University School of Medicine, Durham, North Carolina 27710, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Abhinav Srinath
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Sharbel Romanos
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Ying Li
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Chang Chen
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Aileen A. Ren
- Department of Medicine and Cardiovascular Institute,
University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia PA 19104
| | - Mark L. Kahn
- Department of Medicine and Cardiovascular Institute,
University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia PA 19104
| | - Issam A. Awad
- Neurovascular Surgery Program, Department of Neurological
Surgery, The University of Chicago Medicine and Biological Sciences, Chicago,
Illinois, USA
| | - Douglas A. Marchuk
- Department of Molecular Genetics and Microbiology, Duke
University School of Medicine, Durham, North Carolina 27710, USA
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6
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Snellings DA, Hong CC, Ren AA, Lopez-Ramirez MA, Girard R, Srinath A, Marchuk DA, Ginsberg MH, Awad IA, Kahn ML. Cerebral Cavernous Malformation: From Mechanism to Therapy. Circ Res 2021; 129:195-215. [PMID: 34166073 DOI: 10.1161/circresaha.121.318174] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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] [Indexed: 12/17/2022]
Abstract
Cerebral cavernous malformations are acquired vascular anomalies that constitute a common cause of central nervous system hemorrhage and stroke. The past 2 decades have seen a remarkable increase in our understanding of the pathogenesis of this vascular disease. This new knowledge spans genetic causes of sporadic and familial forms of the disease, molecular signaling changes in vascular endothelial cells that underlie the disease, unexpectedly strong environmental effects on disease pathogenesis, and drivers of disease end points such as hemorrhage. These novel insights are the integrated product of human clinical studies, human genetic studies, studies in mouse and zebrafish genetic models, and basic molecular and cellular studies. This review addresses the genetic and molecular underpinnings of cerebral cavernous malformation disease, the mechanisms that lead to lesion hemorrhage, and emerging biomarkers and therapies for clinical treatment of cerebral cavernous malformation disease. It may also serve as an example for how focused basic and clinical investigation and emerging technologies can rapidly unravel a complex disease mechanism.
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Affiliation(s)
- Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC (D.A.S., D.A.M.)
| | - Courtney C Hong
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia (C.C.H., A.A.R., M.L.K.)
| | - Aileen A Ren
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia (C.C.H., A.A.R., M.L.K.)
| | - Miguel A Lopez-Ramirez
- Department of Medicine (M.A.L.-R., M.H.G.), University of California, San Diego, La Jolla.,Department of Pharmacology (M.A.L.-R.), University of California, San Diego, La Jolla
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois
| | - Abhinav Srinath
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC (D.A.S., D.A.M.)
| | - Mark H Ginsberg
- Department of Medicine (M.A.L.-R., M.H.G.), University of California, San Diego, La Jolla
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, Illinois
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia (C.C.H., A.A.R., M.L.K.)
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7
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Ren AA, Snellings DA, Su YS, Hong CC, Castro M, Tang AT, Detter MR, Hobson N, Girard R, Romanos S, Lightle R, Moore T, Shenkar R, Benavides C, Beaman MM, Müller-Fielitz H, Chen M, Mericko P, Yang J, Sung DC, Lawton MT, Ruppert JM, Schwaninger M, Körbelin J, Potente M, Awad IA, Marchuk DA, Kahn ML. PIK3CA and CCM mutations fuel cavernomas through a cancer-like mechanism. Nature 2021; 594:271-276. [PMID: 33910229 PMCID: PMC8626098 DOI: 10.1038/s41586-021-03562-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [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: 08/25/2020] [Accepted: 04/16/2021] [Indexed: 02/02/2023]
Abstract
Vascular malformations are thought to be monogenic disorders that result in dysregulated growth of blood vessels. In the brain, cerebral cavernous malformations (CCMs) arise owing to inactivation of the endothelial CCM protein complex, which is required to dampen the activity of the kinase MEKK31-4. Environmental factors can explain differences in the natural history of CCMs between individuals5, but why single CCMs often exhibit sudden, rapid growth, culminating in strokes or seizures, is unknown. Here we show that growth of CCMs requires increased signalling through the phosphatidylinositol-3-kinase (PI3K)-mTOR pathway as well as loss of function of the CCM complex. We identify somatic gain-of-function mutations in PIK3CA and loss-of-function mutations in the CCM complex in the same cells in a majority of human CCMs. Using mouse models, we show that growth of CCMs requires both PI3K gain of function and CCM loss of function in endothelial cells, and that both CCM loss of function and increased expression of the transcription factor KLF4 (a downstream effector of MEKK3) augment mTOR signalling in endothelial cells. Consistent with these findings, the mTORC1 inhibitor rapamycin effectively blocks the formation of CCMs in mouse models. We establish a three-hit mechanism analogous to cancer, in which aggressive vascular malformations arise through the loss of vascular 'suppressor genes' that constrain vessel growth and gain of a vascular 'oncogene' that stimulates excess vessel growth. These findings suggest that aggressive CCMs could be treated using clinically approved mTORC1 inhibitors.
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MESH Headings
- Animals
- Animals, Newborn
- Class I Phosphatidylinositol 3-Kinases/genetics
- Class I Phosphatidylinositol 3-Kinases/metabolism
- Disease Models, Animal
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Gain of Function Mutation
- Hemangioma, Cavernous, Central Nervous System/blood supply
- Hemangioma, Cavernous, Central Nervous System/genetics
- Hemangioma, Cavernous, Central Nervous System/metabolism
- Hemangioma, Cavernous, Central Nervous System/pathology
- Humans
- Kruppel-Like Factor 4
- Kruppel-Like Transcription Factors/metabolism
- Loss of Function Mutation
- MAP Kinase Kinase Kinase 3/metabolism
- Male
- Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors
- Mechanistic Target of Rapamycin Complex 1/metabolism
- Mice
- Mutation
- Neoplasms/blood supply
- Neoplasms/genetics
- Neoplasms/pathology
- Sirolimus/pharmacology
- TOR Serine-Threonine Kinases/metabolism
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Affiliation(s)
- Aileen A Ren
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel A Snellings
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Yourong S Su
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Courtney C Hong
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Marco Castro
- Angiogenesis and Metabolism Laboratory, Max Planck institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew R Detter
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Nicholas Hobson
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Romuald Girard
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Sharbel Romanos
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Christian Benavides
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - M Makenzie Beaman
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Helge Müller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Mei Chen
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Patricia Mericko
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Jisheng Yang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Derek C Sung
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael T Lawton
- Department of Neurosurgery, The Barrow Neurological Institute, Phoenix, AZ, USA
| | | | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Jakob Körbelin
- University Medical Center Hamburg-Eppendorf, Department of Oncology, Hematology and Bone Marrow Transplantation, Hamburg, Germany
| | - Michael Potente
- Angiogenesis and Metabolism Laboratory, Max Planck institute for Heart and Lung Research, Bad Nauheim, Germany
- Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Issam A Awad
- Neurovascular Surgery Program, Section of Neurosurgery, Department of Surgery, The University of Chicago Medicine and Biological Sciences, Chicago, IL, USA
| | - Douglas A Marchuk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Snellings DA, Gallione CJ, Clark DS, Vozoris NT, Faughnan ME, Marchuk DA. Somatic Mutations in Vascular Malformations of Hereditary Hemorrhagic Telangiectasia Result in Bi-allelic Loss of ENG or ACVRL1. Am J Hum Genet 2019; 105:894-906. [PMID: 31630786 DOI: 10.1016/j.ajhg.2019.09.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [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: 08/09/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is a Mendelian disease characterized by vascular malformations (VMs) including visceral arteriovenous malformations and mucosal telangiectasia. HHT is caused by loss-of-function (LoF) mutations in one of three genes, ENG, ACVRL1, or SMAD4, and is inherited as an autosomal-dominant condition. Intriguingly, the constitutional mutation causing HHT is present throughout the body, yet the multiple VMs in individuals with HHT occur focally, rather than manifesting as a systemic vascular defect. This disconnect between genotype and phenotype suggests that a local event is necessary for the development of VMs. We investigated the hypothesis that local somatic mutations seed the formation HHT-related telangiectasia in a genetic two-hit mechanism. We identified low-frequency somatic mutations in 9/19 telangiectasia through the use of next-generation sequencing. We established phase for seven of nine samples, which confirms that the germline and somatic mutations in all seven samples exist in trans configuration; this is consistent with a genetic two-hit mechanism. These combined data suggest that bi-allelic loss of ENG or ACVRL1 may be a required event in the development of telangiectasia, and that rather than haploinsufficiency, VMs in HHT are caused by a Knudsonian two-hit mechanism.
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Affiliation(s)
- Daniel A Snellings
- Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Carol J Gallione
- Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Dewi S Clark
- Toronto HHT Centre, Division of Respirology, St. Michael's Hospital and Li Ka Shing Knowledge Institute, Toronto, ON M5B 1A6, Canada
| | - Nicholas T Vozoris
- Toronto HHT Centre, Division of Respirology, St. Michael's Hospital and Li Ka Shing Knowledge Institute, Toronto, ON M5B 1A6, Canada; Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Marie E Faughnan
- Toronto HHT Centre, Division of Respirology, St. Michael's Hospital and Li Ka Shing Knowledge Institute, Toronto, ON M5B 1A6, Canada; Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Douglas A Marchuk
- Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA.
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9
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Abstract
RATIONALE Vascular malformations arise in vessels throughout the entire body. Causative genetic mutations have been identified for many of these diseases; however, little is known about the mutant cell lineage within these malformations. OBJECTIVE We utilize an inducible mouse model of cerebral cavernous malformations (CCMs) coupled with a multicolor fluorescent reporter to visualize the contribution of mutant endothelial cells (ECs) to the malformation. METHODS AND RESULTS We combined a Ccm3 mouse model with the confetti fluorescent reporter to simultaneously delete Ccm3 and label the mutant EC with 1 of 4 possible colors. We acquired Z-series confocal images from serial brain sections and created 3-dimensional reconstructions of entire CCMs to visualize mutant ECs during CCM development. We observed a pronounced pattern of CCMs lined with mutant ECs labeled with a single confetti color (n=42). The close 3-dimensional distribution, as determined by the nearest neighbor analysis, of the clonally dominant ECs within the CCM was statistically different than the background confetti labeling of ECs in non-CCM control brain slices as well as a computer simulation ( P<0.001). Many of the small (<100 μm diameter) CCMs consisted, almost exclusively, of the clonally dominant mutant ECs labeled with the same confetti color, whereas the large (>100 μm diameter) CCMs contained both the clonally dominant mutant cells and wild-type ECs. We propose of model of CCM development in which an EC acquires a second somatic mutation, undergoes clonal expansion to initiate CCM formation, and then incorporates neighboring wild-type ECs to increase the size of the malformation. CONCLUSIONS This is the first study to visualize, with single-cell resolution, the clonal expansion of mutant ECs within CCMs. The incorporation of wild-type ECs into the growing malformation presents another series of cellular events whose elucidation would enhance our understanding of CCMs and may provide novel therapeutic opportunities.
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Affiliation(s)
- Matthew R Detter
- From the Molecular Genetics and Microbiology Department (M.R.D., D.A.S., D.A.M.), Duke University School of Medicine, Durham, NC.,Medical Scientist Training Program (M.R.D.), Duke University School of Medicine, Durham, NC
| | - Daniel A Snellings
- From the Molecular Genetics and Microbiology Department (M.R.D., D.A.S., D.A.M.), Duke University School of Medicine, Durham, NC
| | - Douglas A Marchuk
- From the Molecular Genetics and Microbiology Department (M.R.D., D.A.S., D.A.M.), Duke University School of Medicine, Durham, NC
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