60 results on '"Timms AE"'
Search Results
2. Genetic testing for haemochromatosis in patients with chondrocalcinosis. (Concise Report)
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Timms, AE, Sathananthan, R, Bradbury, L, Athanasou, NA, and Brown, MA
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Genetic disorders -- Diagnosis -- Genetic aspects ,Hemochromatosis -- Diagnosis -- Genetic aspects ,Chondrocalcinosis -- Genetic aspects -- Diagnosis ,Health ,Diagnosis ,Genetic aspects - Abstract
Hereditary haemochromatosis (HH) is the most common lethal monogenic human disease, affecting roughly 1 in 300 white northern Europeans. Homozygosity for the C282Y polymorphism within the HFE gene causes more [...]
- Published
- 2002
3. The IL1 gene cluster is a major locus determining susceptibility to Ankylosing spondylitis
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Timms, AE, Crane, AM, Sims, AM, Bradbury, L, Beynon, O, Coyne, MRE, Herzberg, I, Abbott, A, Cardon, LR, Duff, GR, Calin, A, Wordsworth, P, and Brown, MA
- Published
- 2016
4. Fine-mapping of the IL-1 gene cluster pinpoints genetic associations with ankylosing spondylitis
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Sims, AM, Timms, AE, Pointon, JJ, Bradbury, LA, Wordsworth, BP, and Brown, MA
- Published
- 2016
5. Transcriptomic Signatures of Single-Suture Craniosynostosis Phenotypes.
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Lapehn S, Gustafson JA, Timms AE, Cunningham ML, and Paquette AG
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- Male, Female, Humans, Transcriptome, Skull, Sutures, Cranial Sutures abnormalities, Craniosynostoses genetics
- Abstract
Craniosynostosis is a birth defect where calvarial sutures close prematurely, as part of a genetic syndrome or independently, with unknown cause. This study aimed to identify differences in gene expression in primary calvarial cell lines derived from patients with four phenotypes of single-suture craniosynostosis, compared to controls. Calvarial bone samples (N = 388 cases/85 controls) were collected from clinical sites during reconstructive skull surgery. Primary cell lines were then derived from the tissue and used for RNA sequencing. Linear models were fit to estimate covariate adjusted associations between gene expression and four phenotypes of single-suture craniosynostosis (lambdoid, metopic, sagittal, and coronal), compared to controls. Sex-stratified analysis was also performed for each phenotype. Differentially expressed genes (DEGs) included 72 genes associated with coronal, 90 genes associated with sagittal, 103 genes associated with metopic, and 33 genes associated with lambdoid craniosynostosis. The sex-stratified analysis revealed more DEGs in males (98) than females (4). There were 16 DEGs that were homeobox (HOX) genes. Three TFs (SUZ12, EZH2, AR) significantly regulated expression of DEGs in one or more phenotypes. Pathway analysis identified four KEGG pathways associated with at least one phenotype of craniosynostosis. Together, this work suggests unique molecular mechanisms related to craniosynostosis phenotype and fetal sex.
- Published
- 2023
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6. Monoallelic and biallelic mutations in RELN underlie a graded series of neurodevelopmental disorders.
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Di Donato N, Guerrini R, Billington CJ, Barkovich AJ, Dinkel P, Freri E, Heide M, Gershon ES, Gertler TS, Hopkin RJ, Jacob S, Keedy SK, Kooshavar D, Lockhart PJ, Lohmann DR, Mahmoud IG, Parrini E, Schrock E, Severi G, Timms AE, Webster RI, Willis MJH, Zaki MS, Gleeson JG, Leventer RJ, and Dobyns WB
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- Adult, Cerebellum abnormalities, Child, Developmental Disabilities genetics, Humans, Mutation, Nervous System Malformations, Lissencephaly complications, Reelin Protein genetics
- Abstract
Reelin, a large extracellular protein, plays several critical roles in brain development and function. It is encoded by RELN, first identified as the gene disrupted in the reeler mouse, a classic neurological mutant exhibiting ataxia, tremors and a 'reeling' gait. In humans, biallelic variants in RELN have been associated with a recessive lissencephaly variant with cerebellar hypoplasia, which matches well with the homozygous mouse mutant that has abnormal cortical structure, small hippocampi and severe cerebellar hypoplasia. Despite the large size of the gene, only 11 individuals with RELN-related lissencephaly with cerebellar hypoplasia from six families have previously been reported. Heterozygous carriers in these families were briefly reported as unaffected, although putative loss-of-function variants are practically absent in the population (probability of loss of function intolerance = 1). Here we present data on seven individuals from four families with biallelic and 13 individuals from seven families with monoallelic (heterozygous) variants of RELN and frontotemporal or temporal-predominant lissencephaly variant. Some individuals with monoallelic variants have moderate frontotemporal lissencephaly, but with normal cerebellar structure and intellectual disability with severe behavioural dysfunction. However, one adult had abnormal MRI with normal intelligence and neurological profile. Thorough literature analysis supports a causal role for monoallelic RELN variants in four seemingly distinct phenotypes including frontotemporal lissencephaly, epilepsy, autism and probably schizophrenia. Notably, we observed a significantly higher proportion of loss-of-function variants in the biallelic compared to the monoallelic cohort, where the variant spectrum included missense and splice-site variants. We assessed the impact of two canonical splice-site variants observed as biallelic or monoallelic variants in individuals with moderately affected or normal cerebellum and demonstrated exon skipping causing in-frame loss of 46 or 52 amino acids in the central RELN domain. Previously reported functional studies demonstrated severe reduction in overall RELN secretion caused by heterozygous missense variants p.Cys539Arg and p.Arg3207Cys associated with lissencephaly suggesting a dominant-negative effect. We conclude that biallelic variants resulting in complete absence of RELN expression are associated with a consistent and severe phenotype that includes cerebellar hypoplasia. However, reduced expression of RELN remains sufficient to maintain nearly normal cerebellar structure. Monoallelic variants are associated with incomplete penetrance and variable expressivity even within the same family and may have dominant-negative effects. Reduced RELN secretion in heterozygous individuals affects only cortical structure whereas the cerebellum remains intact. Our data expand the spectrum of RELN-related neurodevelopmental disorders ranging from lethal brain malformations to adult phenotypes with normal brain imaging., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2022
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7. Anti-tumor activity of a T-helper 1 multiantigen vaccine in a murine model of prostate cancer.
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Cecil DL, Curtis B, Gad E, Gormley M, Timms AE, Corulli L, Bos R, Damle RN, Sepulveda MA, and Disis ML
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- Animals, Antigens, Disease Models, Animal, Epitopes, Epitopes, T-Lymphocyte, Humans, Male, Mice, T-Lymphocytes, Cancer Vaccines, Prostatic Neoplasms therapy
- Abstract
Prostate cancer is one of the few malignancies that includes vaccination as a treatment modality. Elements of an effective cancer vaccine should include the ability to elicit a Type I T-cell response and target multiple antigenic proteins expressed early in the disease. Using existing gene datasets encompassing normal prostate tissue and tumors with Gleason Score ≤ 6 and ≥ 8, 10 genes were identified that were upregulated and conserved in prostate cancer regardless of the aggressiveness of disease. These genes encoded proteins also expressed in prostatic intraepithelial neoplasia. Putative Class II epitopes derived from these proteins were predicted by a combination of algorithms and, using human peripheral blood, epitopes which selectively elicited IFN-γ or IL-10 dominant antigen specific cytokine secretion were determined. Th1 selective epitopes were identified for eight antigens. Epitopes from three antigens elicited Th1 dominant immunity in mice; PSMA, HPN, and AMACR. Each single antigen vaccine demonstrated significant anti-tumor activity inhibiting growth of implanted Myc-Cap cells after immunization as compared to control. Immunization with the combination of antigens, however, was superior to each alone in controlling tumor growth. When vaccination occurred simultaneously to tumor implant, multiantigen immunized mice had significantly smaller tumors than controls (p = 0.002) and a significantly improved overall survival (p = 0.0006). This multiantigen vaccine shows anti-tumor activity in a murine model of prostate cancer., (© 2022. The Author(s).)
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- 2022
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8. Profiling PI3K-AKT-MTOR variants in focal brain malformations reveals new insights for diagnostic care.
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Pirozzi F, Berkseth M, Shear R, Gonzalez L, Timms AE, Sulc J, Pao E, Oyama N, Forzano F, Conti V, Guerrini R, Doherty ES, Saitta SC, Lockwood CM, Pritchard CC, Dobyns WB, Novotny E, Wright JNN, Saneto RP, Friedman S, Hauptman J, Ojemann J, Kapur RP, and Mirzaa GM
- Subjects
- Brain pathology, Child, Class I Phosphatidylinositol 3-Kinases genetics, Class I Phosphatidylinositol 3-Kinases metabolism, Humans, Mutation, Phosphatidylinositol 3-Kinases genetics, Phosphatidylinositol 3-Kinases metabolism, Proto-Oncogene Proteins c-akt genetics, TOR Serine-Threonine Kinases genetics, TOR Serine-Threonine Kinases metabolism, Drug Resistant Epilepsy metabolism, Epilepsy genetics, Hemimegalencephaly genetics, Hemimegalencephaly metabolism, Hemimegalencephaly pathology, Malformations of Cortical Development diagnostic imaging, Malformations of Cortical Development genetics
- Abstract
Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology., (© The Author(s) (2022). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2022
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9. Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal cis-Regulatory Elements.
- Author
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VandenBosch LS, Luu K, Timms AE, Challam S, Wu Y, Lee AY, and Cherry TJ
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- Humans, Nucleotides, Phylogeny, Retina, Transcription Factors genetics, Transcription Factors metabolism, Machine Learning, Retinal Diseases genetics
- Abstract
Purpose: Prior studies have demonstrated the significance of specific cis-regulatory variants in retinal disease; however, determining the functional impact of regulatory variants remains a major challenge. In this study, we utilized a machine learning approach, trained on epigenomic data from the adult human retina, to systematically quantify the predicted impact of cis-regulatory variants., Methods: We used human retinal DNA accessibility data (ATAC-seq) to determine a set of 18.9k high-confidence, putative cis-regulatory elements. Eighty percent of these elements were used to train a machine learning model utilizing a gapped k-mer support vector machine-based approach. In silico saturation mutagenesis and variant scoring was applied to predict the functional impact of all potential single nucleotide variants within cis-regulatory elements. Impact scores were tested in a 20% hold-out dataset and compared to allele population frequency, phylogenetic conservation, transcription factor (TF) binding motifs, and existing massively parallel reporter assay data., Results: We generated a model that distinguishes between human retinal regulatory elements and negative test sequences with 95% accuracy. Among a hold-out test set of 3.7k human retinal CREs, all possible single nucleotide variants were scored. Variants with negative impact scores correlated with higher phylogenetic conservation of the reference allele, disruption of predicted TF binding motifs, and massively parallel reporter expression., Conclusions: We demonstrated the utility of human retinal epigenomic data to train a machine learning model for the purpose of predicting the impact of non-coding regulatory sequence variants. Our model accurately scored sequences and predicted putative transcription factor binding motifs. This approach has the potential to expedite the characterization of pathogenic non-coding sequence variants in the context of unexplained retinal disease., Translational Relevance: This workflow and resulting dataset serve as a promising genomic tool to facilitate the clinical prioritization of functionally disruptive non-coding mutations in the retina.
- Published
- 2022
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10. Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids.
- Author
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Thomas ED, Timms AE, Giles S, Harkins-Perry S, Lyu P, Hoang T, Qian J, Jackson VE, Bahlo M, Blackshaw S, Friedlander M, Eade K, and Cherry TJ
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- Adult, Chromatin genetics, Humans, Regulatory Sequences, Nucleic Acid, Sequence Analysis, RNA, Organoids, Retina
- Abstract
Cis-regulatory elements (CREs) play a critical role in the development and disease-states of all human cell types. In the retina, CREs have been implicated in several inherited disorders. To better characterize human retinal CREs, we performed single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) and single-nucleus RNA sequencing (snRNA-seq) on the developing and adult human retina and on induced pluripotent stem cell (iPSC)-derived retinal organoids. These analyses identified developmentally dynamic, cell-class-specific CREs, enriched transcription-factor-binding motifs, and putative target genes. CREs in the retina and organoids are highly correlated at the single-cell level, and this supports the use of organoids as a model for studying disease-associated CREs. As a proof of concept, we disrupted a disease-associated CRE at 5q14.3, confirming its principal target gene as the miR-9-2 primary transcript and demonstrating its role in neurogenesis and gene regulation in mature glia. This study provides a resource for characterizing human retinal CREs and showcases organoids as a model to study the function of CREs that influence development and disease., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 Elsevier Inc. All rights reserved.)
- Published
- 2022
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11. Activated interleukin-7 receptor signaling drives B-cell acute lymphoblastic leukemia in mice.
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Thomas KR, Allenspach EJ, Camp ND, Wray-Dutra MN, Khim S, Zielinska-Kwiatkowska A, Timms AE, Loftus JP, Liggitt HD, Georgopoulos K, Tasian SK, James RG, and Rawlings DJ
- Subjects
- Animals, Apoptosis, Cell Proliferation, Humans, Mice, Mice, Inbred NOD, Mice, SCID, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma etiology, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma metabolism, Receptors, Interleukin-7 genetics, Tumor Cells, Cultured, Xenograft Model Antitumor Assays, Gene Expression Regulation, Leukemic, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma pathology, Receptors, Interleukin-7 metabolism
- Abstract
Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL) is a high-risk subtype of B-ALL often associated with genetic variants that alter cytokine receptor signaling, including mutations in the interleukin-7 receptor (IL7R). To investigate whether IL7R variants are leukemia-initiating, we built mouse models expressing activated Il7r (aIL7R). B-cell intrinsic aIL7R mice developed spontaneous B-ALL, demonstrating sufficiency of Il7r activating mutations in leukemogenesis. Concomitant introduction of a knock-out allele in the associated adapter protein Lnk (encoded by Sh2b3) or a dominant-negative variant of the transcription factor Ikaros (Ikzf1) increased disease penetrance. The resulting murine leukemias displayed monoclonality and recurrent somatic Kras mutations and efficiently engrafted into immunocompetent mice. Phosphoproteomic analyses of aIL7R leukemic cells revealed constitutive Stat5 signaling and B cell receptor (BCR)-like signaling despite the absence of surface pre-BCR. Finally, in vitro treatment of aIL7R leukemic B-cells with Jak, mTOR, or Syk inhibitors blocked growth, confirming that each pathway is active in this mouse model of IL7R-driven B-ALL., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)
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- 2022
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12. The Autoimmune Risk R262W Variant of the Adaptor SH2B3 Improves Survival in Sepsis.
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Allenspach EJ, Shubin NJ, Cerosaletti K, Mikacenic C, Gorman JA, MacQuivey MA, Rosen ABI, Timms AE, Wray-Dutra MN, Niino K, Liggitt D, Wurfel MM, Buckner JH, Piliponsky AM, and Rawlings DJ
- Subjects
- Adaptor Proteins, Signal Transducing genetics, Adult, Animals, Disease Models, Animal, Humans, Mice, Mice, Congenic, Mice, Inbred C57BL, Mice, Knockout, Mice, Transgenic, Polymorphism, Single Nucleotide genetics, Sepsis genetics, Adaptor Proteins, Signal Transducing immunology, Sepsis immunology
- Abstract
The single-nucleotide polymorphism (SNP) rs3184504 is broadly associated with increased risk for multiple autoimmune and cardiovascular diseases. Although the allele is uniquely enriched in European descent, the mechanism for the widespread selective sweep is not clear. In this study, we find the rs3184504*T allele had a strong association with reduced mortality in a human sepsis cohort. The rs3184504*T allele associates with a loss-of-function amino acid change (p.R262W) in the adaptor protein SH2B3, a likely causal variant. To better understand the role of SH2B3 in sepsis, we used mouse modeling and challenged SH2B3-deficient mice with a polymicrobial cecal-ligation puncture (CLP) procedure. We found SH2B3 deficiency improved survival and morbidity with less organ damage and earlier bacterial clearance compared with control mice. The peritoneal infiltrating cells exhibited augmented phagocytosis in Sh2b3
-/- mice with enriched recruitment of Ly6Chi inflammatory monocytes despite equivalent or reduced chemokine expression. Rapid cycling of monocytes and progenitors occurred uniquely in the Sh2b3-/- mice following CLP, suggesting augmented myelopoiesis. To model the hypomorphic autoimmune risk allele, we created a novel knockin mouse harboring a similar point mutation in the murine pleckstrin homology domain of SH2B3. At baseline, phenotypic changes suggested a hypomorphic allele. In the CLP model, homozygous knockin mice displayed improved mortality and morbidity compared with wild-type or heterozygous mice. Collectively, these data suggest that hypomorphic SH2B3 improves the sepsis response and that balancing selection likely contributed to the relative frequency of the autoimmune risk variant., (Copyright © 2021 by The American Association of Immunologists, Inc.)- Published
- 2021
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13. Gene regulatory networks controlling temporal patterning, neurogenesis, and cell-fate specification in mammalian retina.
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Lyu P, Hoang T, Santiago CP, Thomas ED, Timms AE, Appel H, Gimmen M, Le N, Jiang L, Kim DW, Chen S, Espinoza DF, Telger AE, Weir K, Clark BS, Cherry TJ, Qian J, and Blackshaw S
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- Animals, Cell Differentiation genetics, Eye Proteins metabolism, Female, Gene Expression genetics, Gene Expression Regulation, Developmental genetics, Gene Regulatory Networks genetics, Homeodomain Proteins metabolism, Humans, Male, Mice embryology, NFI Transcription Factors metabolism, Retinal Neurons metabolism, Retinal Rod Photoreceptor Cells metabolism, Trans-Activators metabolism, Body Patterning genetics, Cell Lineage genetics, Neurogenesis genetics, Retina embryology
- Abstract
Gene regulatory networks (GRNs), consisting of transcription factors and their target sites, control neurogenesis and cell-fate specification in the developing central nervous system. In this study, we use integrated single-cell RNA and single-cell ATAC sequencing (scATAC-seq) analysis in developing mouse and human retina to identify multiple interconnected, evolutionarily conserved GRNs composed of cell-type-specific transcription factors that both activate genes within their own network and inhibit genes in other networks. These GRNs control temporal patterning in primary progenitors, regulate transition from primary to neurogenic progenitors, and drive specification of each major retinal cell type. We confirm that NFI transcription factors selectively activate expression of genes promoting late-stage temporal identity in primary retinal progenitors and identify other transcription factors that regulate rod photoreceptor specification in postnatal retina. This study inventories cis- and trans-acting factors that control retinal development and can guide cell-based therapies aimed at replacing retinal neurons lost to disease., Competing Interests: Declaration of interests S.B. co-founded and is a shareholder of CDI Labs, LLC. S.B. is also a consultant for Third Rock Ventures, LLC., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2021
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14. Spiny mice activate unique transcriptional programs after severe kidney injury regenerating organ function without fibrosis.
- Author
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Okamura DM, Brewer CM, Wakenight P, Bahrami N, Bernardi K, Tran A, Olson J, Shi X, Yeh SY, Piliponsky A, Collins SJ, Nguyen ED, Timms AE, MacDonald JW, Bammler TK, Nelson BR, Millen KJ, Beier DR, and Majesky MW
- Abstract
Fibrosis-driven solid organ failure is an enormous burden on global health. Spiny mice ( Acomys ) are terrestrial mammals that can regenerate severe skin wounds without scars to avoid predation. Whether spiny mice also regenerate internal organ injuries is unknown. Here, we show that despite equivalent acute obstructive or ischemic kidney injury, spiny mice fully regenerate nephron structure and organ function without fibrosis, whereas C57Bl/6 or CD1 mice progress to complete organ failure with extensive renal fibrosis. Two mechanisms for vertebrate regeneration have been proposed that emphasize either extrinsic (pro-regenerative macrophages) or intrinsic (surviving cells of the organ itself) controls. Comparative transcriptome analysis revealed that the Acomys genome appears poised at the time of injury to initiate regeneration by surviving kidney cells, whereas macrophage accumulation was not detected until about day 7. Thus, we provide evidence for rapid activation of a gene expression signature for regenerative wound healing in the spiny mouse kidney., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)
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- 2021
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15. Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.
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Weerts MJA, Lanko K, Guzmán-Vega FJ, Jackson A, Ramakrishnan R, Cardona-Londoño KJ, Peña-Guerra KA, van Bever Y, van Paassen BW, Kievit A, van Slegtenhorst M, Allen NM, Kehoe CM, Robinson HK, Pang L, Banu SH, Zaman M, Efthymiou S, Houlden H, Järvelä I, Lauronen L, Määttä T, Schrauwen I, Leal SM, Ruivenkamp CAL, Barge-Schaapveld DQCM, Peeters-Scholte CMPCD, Galehdari H, Mazaheri N, Sisodiya SM, Harrison V, Sun A, Thies J, Pedroza LA, Lara-Taranchenko Y, Chinn IK, Lupski JR, Garza-Flores A, McGlothlin J, Yang L, Huang S, Wang X, Jewett T, Rosso G, Lin X, Mohammed S, Merritt JL 2nd, Mirzaa GM, Timms AE, Scheck J, Elting MW, Polstra AM, Schenck L, Ruzhnikov MRZ, Vetro A, Montomoli M, Guerrini R, Koboldt DC, Mosher TM, Pastore MT, McBride KL, Peng J, Pan Z, Willemsen M, Koning S, Turnpenny PD, de Vries BBA, Gilissen C, Pfundt R, Lees M, Braddock SR, Klemp KC, Vansenne F, van Gijn ME, Quindipan C, Deardorff MA, Hamm JA, Putnam AM, Baud R, Walsh L, Lynch SA, Baptista J, Person RE, Monaghan KG, Crunk A, Keller-Ramey J, Reich A, Elloumi HZ, Alders M, Kerkhof J, McConkey H, Haghshenas S, Maroofian R, Sadikovic B, Banka S, Arold ST, and Barakat TS
- Subjects
- Humans, Male, Phenotype, Seizures diagnosis, Seizures genetics, Epilepsy diagnosis, Epilepsy genetics, Histone-Lysine N-Methyltransferase genetics, Intellectual Disability diagnosis, Intellectual Disability genetics, Neurodevelopmental Disorders diagnosis, Neurodevelopmental Disorders genetics
- Abstract
Purpose: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort., Methods: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays., Results: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants., Conclusion: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome., (© 2021. The Author(s).)
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- 2021
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16. Evidence of disrupted rhombic lip development in the pathogenesis of Dandy-Walker malformation.
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Haldipur P, Bernardo S, Aldinger KA, Sivakumar T, Millman J, Sjoboen AH, Dang D, Dubocanin D, Deng M, Timms AE, Davis BD, Plummer JT, Mankad K, Oztekin O, Manganaro L, Guimiot F, Adle-Biassette H, Russo R, Siebert JR, Kidron D, Petrilli G, Roux N, Razavi F, Glass IA, Di Gioia C, Silvestri E, and Millen KJ
- Subjects
- Case-Control Studies, Cerebellum embryology, Cerebellum pathology, Developmental Disabilities pathology, Humans, Infant, Newborn, Cerebellum abnormalities, Dandy-Walker Syndrome embryology, Dandy-Walker Syndrome pathology, Fetal Development physiology, Fetus pathology, Nervous System Malformations embryology, Nervous System Malformations pathology
- Abstract
Dandy-Walker malformation (DWM) and Cerebellar vermis hypoplasia (CVH) are commonly recognized human cerebellar malformations diagnosed following ultrasound and antenatal or postnatal MRI. Specific radiological criteria are used to distinguish them, yet little is known about their differential developmental disease mechanisms. We acquired prenatal cases diagnosed as DWM and CVH and studied cerebellar morphobiometry followed by histological and immunohistochemical analyses. This was supplemented by laser capture microdissection and RNA-sequencing of the cerebellar rhombic lip, a transient progenitor zone, to assess the altered transcriptome of DWM vs control samples. Our radiological findings confirm that the cases studied fall within the accepted biometric range of DWM. Our histopathological analysis points to reduced foliation and inferior vermian hypoplasia as common features in all examined DWM cases. We also find that the rhombic lip, a dorsal stem cell zone that drives the growth and maintenance of the posterior vermis is specifically disrupted in DWM, with reduced proliferation and self-renewal of the progenitor pool, and altered vasculature, all confirmed by transcriptomics analysis. We propose a unified model for the developmental pathogenesis of DWM. We hypothesize that rhombic lip development is disrupted through either aberrant vascularization and/or direct insult which causes reduced proliferation and failed expansion of the rhombic lip progenitor pool leading to disproportionate hypoplasia and dysplasia of the inferior vermis. Timing of insult to the developing rhombic lip (before or after 14 PCW) dictates the extent of hypoplasia and distinguishes DWM from CVH., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2021
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17. Haploinsufficiency of SF3B2 causes craniofacial microsomia.
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Timberlake AT, Griffin C, Heike CL, Hing AV, Cunningham ML, Chitayat D, Davis MR, Doust SJ, Drake AF, Duenas-Roque MM, Goldblatt J, Gustafson JA, Hurtado-Villa P, Johns A, Karp N, Laing NG, Magee L, Mullegama SV, Pachajoa H, Porras-Hurtado GL, Schnur RE, Slee J, Singer SL, Staffenberg DA, Timms AE, Wise CA, Zarante I, Saint-Jeannet JP, and Luquetti DV
- Subjects
- Adolescent, Adult, Animals, Child, Exome genetics, Female, Genetic Association Studies, Goldenhar Syndrome pathology, Humans, Infant, Male, Mutation, Neural Crest growth & development, Neural Crest pathology, Pedigree, Spliceosomes genetics, Xenopus laevis, Goldenhar Syndrome genetics, Haploinsufficiency, RNA Splicing Factors genetics
- Abstract
Craniofacial microsomia (CFM) is the second most common congenital facial anomaly, yet its genetic etiology remains unknown. We perform whole-exome or genome sequencing of 146 kindreds with sporadic (n = 138) or familial (n = 8) CFM, identifying a highly significant burden of loss of function variants in SF3B2 (P = 3.8 × 10
-10 ), a component of the U2 small nuclear ribonucleoprotein complex, in probands. We describe twenty individuals from seven kindreds harboring de novo or transmitted haploinsufficient variants in SF3B2. Probands display mandibular hypoplasia, microtia, facial and preauricular tags, epibulbar dermoids, lateral oral clefts in addition to skeletal and cardiac abnormalities. Targeted morpholino knockdown of SF3B2 in Xenopus results in disruption of cranial neural crest precursor formation and subsequent craniofacial cartilage defects, supporting a link between spliceosome mutations and impaired neural crest development in congenital craniofacial disease. The results establish haploinsufficient variants in SF3B2 as the most prevalent genetic cause of CFM, explaining ~3% of sporadic and ~25% of familial cases., (© 2021. The Author(s).)- Published
- 2021
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18. Spatial and cell type transcriptional landscape of human cerebellar development.
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Aldinger KA, Thomson Z, Phelps IG, Haldipur P, Deng M, Timms AE, Hirano M, Santpere G, Roco C, Rosenberg AB, Lorente-Galdos B, Gulden FO, O'Day D, Overman LM, Lisgo SN, Alexandre P, Sestan N, Doherty D, Dobyns WB, Seelig G, Glass IA, and Millen KJ
- Subjects
- Fetus, Humans, Laser Capture Microdissection, Single-Cell Analysis, Transcriptome, Cerebellum embryology, Neurogenesis
- Abstract
The human neonatal cerebellum is one-fourth of its adult size yet contains the blueprint required to integrate environmental cues with developing motor, cognitive and emotional skills into adulthood. Although mature cerebellar neuroanatomy is well studied, understanding of its developmental origins is limited. In this study, we systematically mapped the molecular, cellular and spatial composition of human fetal cerebellum by combining laser capture microscopy and SPLiT-seq single-nucleus transcriptomics. We profiled functionally distinct regions and gene expression dynamics within cell types and across development. The resulting cell atlas demonstrates that the molecular organization of the cerebellar anlage recapitulates cytoarchitecturally distinct regions and developmentally transient cell types that are distinct from the mouse cerebellum. By mapping genes dominant for pediatric and adult neurological disorders onto our dataset, we identify relevant cell types underlying disease mechanisms. These data provide a resource for probing the cellular basis of human cerebellar development and disease., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2021
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19. MYT1 role in the microtia-craniofacial microsomia spectrum.
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Luquetti DV, Heike CL, Zarante I, Timms AE, Gustafson J, Pachajoa H, Porras-Hurtado GL, Ayala-Ramirez P, Duenas-Roque MM, Jimenez N, Ibanez LM, and Hurtado-Villa P
- Subjects
- Child, Congenital Microtia pathology, Female, Goldenhar Syndrome pathology, Humans, Male, Mutation, Syndrome, Congenital Microtia genetics, DNA-Binding Proteins genetics, Goldenhar Syndrome genetics, Transcription Factors genetics
- Abstract
Background: Craniofacial microsomia (CFM), also known as the oculo-auriculo-vertebral spectrum, comprises a variable phenotype with the most common features including microtia and mandibular hypoplasia on one or both sides, in addition to lateral oral clefts, epibulbar dermoids, cardiac, vertebral, and renal abnormalities. The etiology of CFM is largely unknown. The MYT1 gene has been reported as a candidate based in mutations found in three unrelated individuals. Additional patients with mutations in this gene are required to establish its causality. We present two individuals with CFM that have rare variants in MYT1 contributing to better understand the genotype and phenotype associated with mutations in this gene., Methods/results: We conducted genetic analysis using whole-exome and -genome sequencing in 128 trios with CFM. Two novel MYT1 mutations were identified in two participants. Sanger sequencing was used to confirm these mutations., Conclusion: We identified two additional individuals with CFM who carry rare variants in MYT1, further supporting the presumptive role of this gene in the CFM spectrum., (© 2020 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals LLC.)
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- 2020
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20. Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain.
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Aldinger KA, Timms AE, MacDonald JW, McNamara HK, Herstein JS, Bammler TK, Evgrafov OV, Knowles JA, and Levitt P
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- Cadaver, Female, Humans, Sequence Analysis, RNA, Gyrus Cinguli metabolism, Rett Syndrome metabolism, Temporal Lobe metabolism, Transcriptome
- Abstract
Rett syndrome is an X-linked neurodevelopmental disorder caused by mutation in the methyl-CpG-binding protein 2 gene (MECP2) in the majority of cases. We describe an RNA sequencing dataset of postmortem brain tissue samples from four females clinically diagnosed with Rett syndrome and four age-matched female donors. The dataset contains 16 transcriptomes, including two brain regions, temporal and cingulate cortex, for each individual. We compared our dataset with published transcriptomic analyses of postmortem brain tissue from Rett syndrome and found consistent gene expression alterations among regions of the cerebral cortex. Our data provide a valuable resource to explore the biology of the human brain in Rett syndrome.
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- 2020
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21. Mapping the cis -regulatory architecture of the human retina reveals noncoding genetic variation in disease.
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Cherry TJ, Yang MG, Harmin DA, Tao P, Timms AE, Bauwens M, Allikmets R, Jones EM, Chen R, De Baere E, and Greenberg ME
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- Adult, Animals, DNA Mutational Analysis, Epigenomics, Female, Genetic Variation, Humans, Male, Mice, Middle Aged, Mutation, RNA-Seq, Retina growth & development, Retinal Diseases pathology, Species Specificity, Evolution, Molecular, Gene Expression Regulation, Developmental, Regulatory Sequences, Nucleic Acid genetics, Retina pathology, Retinal Diseases genetics
- Abstract
The interplay of transcription factors and cis -regulatory elements (CREs) orchestrates the dynamic and diverse genetic programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. We took advantage of the retina, a well-characterized region of the CNS known to be affected by pathogenic variants in CREs, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive analysis of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, and retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue-specific gene expression programs and defines regulatory elements with the potential to contribute to Mendelian and complex disorders of human vision., Competing Interests: The authors declare no competing interest.
- Published
- 2020
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22. Genotype correlates with clinical severity in PIK3CA-associated lymphatic malformations.
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Zenner K, Cheng CV, Jensen DM, Timms AE, Shivaram G, Bly R, Ganti S, Whitlock KB, Dobyns WB, Perkins J, and Bennett JT
- Subjects
- Adolescent, Child, Child, Preschool, Female, Humans, Lymphatic Vessels diagnostic imaging, Magnetic Resonance Imaging, Male, Retrospective Studies, Severity of Illness Index, Class I Phosphatidylinositol 3-Kinases genetics, Genotype, Lymphatic Vessels abnormalities, Mutation
- Abstract
Lymphatic malformations (LMs) are congenital, nonneoplastic vascular malformations associated with postzygotic activating PIK3CA mutations. The mutation spectrum within LMs is narrow, with the majority having 1 of 3 hotspot mutations. Despite this relative genetic homogeneity, clinical presentations differ dramatically. We used molecular inversion probes and droplet digital polymerase chain reaction to perform deep, targeted sequencing of PIK3CA in 271 affected and unaffected tissue samples from 81 individuals with isolated LMs and retrospectively collected clinical data. Pathogenic PIK3CA mutations were identified in affected LM tissue in 64 individuals (79%) with isolated LMs, with variant allele fractions (VAFs) ranging from 0.1% to 13%. Initial analyses revealed no correlation between VAF and phenotype variables. Recognizing that different mutations activate PI3K to varying degrees, we developed a metric, the genotype-adjusted VAF (GVAF), to account for differences in mutation strength, and found significantly higher GVAFs in LMs with more severe clinical characteristics including orofacial location or microcystic structure. In addition to providing insight into LM pathogenesis, we believe GVAF may have broad applicability for genotype-phenotype analyses in mosaic disorders.
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- 2019
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23. Spatiotemporal expansion of primary progenitor zones in the developing human cerebellum.
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Haldipur P, Aldinger KA, Bernardo S, Deng M, Timms AE, Overman LM, Winter C, Lisgo SN, Razavi F, Silvestri E, Manganaro L, Adle-Biassette H, Guimiot F, Russo R, Kidron D, Hof PR, Gerrelli D, Lindsay SJ, Dobyns WB, Glass IA, Alexandre P, and Millen KJ
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- Animals, Dandy-Walker Syndrome, Humans, Mice, Nervous System Malformations, Spatio-Temporal Analysis, Species Specificity, Transcriptome, Cerebellum embryology, Cerebellum growth & development, Stem Cells cytology
- Abstract
We present histological and molecular analyses of the developing human cerebellum from 30 days after conception to 9 months after birth. Differences in developmental patterns between humans and mice include spatiotemporal expansion of both ventricular and rhombic lip primary progenitor zones to include subventricular zones containing basal progenitors. The human rhombic lip persists longer through cerebellar development than in the mouse and undergoes morphological changes to form a progenitor pool in the posterior lobule, which is not seen in other organisms, not even in the nonhuman primate the macaque. Disruptions in human rhombic lip development are associated with posterior cerebellar vermis hypoplasia and Dandy-Walker malformation. The presence of these species-specific neural progenitor populations refines our insight into human cerebellar developmental disorders., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
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- 2019
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24. Redefining the Etiologic Landscape of Cerebellar Malformations.
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Aldinger KA, Timms AE, Thomson Z, Mirzaa GM, Bennett JT, Rosenberg AB, Roco CM, Hirano M, Abidi F, Haldipur P, Cheng CV, Collins S, Park K, Zeiger J, Overmann LM, Alkuraya FS, Biesecker LG, Braddock SR, Cathey S, Cho MT, Chung BHY, Everman DB, Zarate YA, Jones JR, Schwartz CE, Goldstein A, Hopkin RJ, Krantz ID, Ladda RL, Leppig KA, McGillivray BC, Sell S, Wusik K, Gleeson JG, Nickerson DA, Bamshad MJ, Gerrelli D, Lisgo SN, Seelig G, Ishak GE, Barkovich AJ, Curry CJ, Glass IA, Millen KJ, Doherty D, and Dobyns WB
- Subjects
- Cerebellum diagnostic imaging, Cohort Studies, Female, Humans, Male, Pregnancy, Cerebellum abnormalities
- Abstract
Cerebellar malformations are diverse congenital anomalies frequently associated with developmental disability. Although genetic and prenatal non-genetic causes have been described, no systematic analysis has been performed. Here, we present a large-exome sequencing study of Dandy-Walker malformation (DWM) and cerebellar hypoplasia (CBLH). We performed exome sequencing in 282 individuals from 100 families with DWM or CBLH, and we established a molecular diagnosis in 36 of 100 families, with a significantly higher yield for CBLH (51%) than for DWM (16%). The 41 variants impact 27 neurodevelopmental-disorder-associated genes, thus demonstrating that CBLH and DWM are often features of monogenic neurodevelopmental disorders. Though only seven monogenic causes (19%) were identified in more than one individual, neuroimaging review of 131 additional individuals confirmed cerebellar abnormalities in 23 of 27 genetic disorders (85%). Prenatal risk factors were frequently found among individuals without a genetic diagnosis (30 of 64 individuals [47%]). Single-cell RNA sequencing of prenatal human cerebellar tissue revealed gene enrichment in neuronal and vascular cell types; this suggests that defective vasculogenesis may disrupt cerebellar development. Further, de novo gain-of-function variants in PDGFRB, a tyrosine kinase receptor essential for vascular progenitor signaling, were associated with CBLH, and this discovery links genetic and non-genetic etiologies. Our results suggest that genetic defects impact specific cerebellar cell types and implicate abnormal vascular development as a mechanism for cerebellar malformations. We also confirmed a major contribution for non-genetic prenatal factors in individuals with cerebellar abnormalities, substantially influencing diagnostic evaluation and counseling regarding recurrence risk and prognosis., (Copyright © 2019 American Society of Human Genetics. All rights reserved.)
- Published
- 2019
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25. Transcriptome profiling reveals activation of inflammation and apoptosis in the neonatal striatum after deep hypothermic circulatory arrest.
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Tu LN, Timms AE, Kibiryeva N, Bittel D, Pastuszko A, Nigam V, and Pastuszko P
- Subjects
- Animals, Animals, Newborn, Apoptosis Regulatory Proteins metabolism, Cytokines metabolism, Neostriatum metabolism, Signal Transduction, Sus scrofa, Apoptosis genetics, Apoptosis Regulatory Proteins genetics, Circulatory Arrest, Deep Hypothermia Induced adverse effects, Cytokines genetics, Gene Expression Profiling, Inflammation Mediators metabolism, Neostriatum pathology, Transcriptome
- Abstract
Objectives: Brain injury, leading to long-term neurodevelopmental deficits, is a major complication in neonates undergoing cardiac surgeries. Because the striatum is one of the most vulnerable brain regions, we used mRNA sequencing to unbiasedly identify transcriptional changes in the striatum after cardiopulmonary bypass and associated deep hypothermic circulatory arrest., Methods: Piglets were subjected to cardiopulmonary bypass with deep hypothermic circulatory arrest at 18°C for 30 minutes and then recovered for 6 hours. mRNA sequencing was performed to compare changes in gene expression between the striatums of sham control and deep hypothermic circulatory arrest brains., Results: We found 124 significantly upregulated genes and 74 significantly downregulated genes in the striatums of the deep hypothermic circulatory arrest group compared with the sham controls. Pathway enrichment analysis demonstrated that inflammation and apoptosis were the strongest pathways activated after surgery. Chemokines CXCL9, CXCL10, and CCL2 were the top upregulated genes with 32.4-fold, 22.2-fold, and 17.6-fold increased expression, respectively, in the deep hypothermic circulatory arrest group compared with sham controls. Concomitantly, genes involved in cell proliferation, cell-cell adhesion, and structural integrity were significantly downregulated in the deep hypothermic circulatory arrest group. Analysis of promoter regions of all upregulated genes revealed over-representation of nuclear factor-kB transcription factor binding sites., Conclusions: Our study provides a comprehensive view of global transcriptional changes in the striatum after deep hypothermic circulatory arrest and found strong activation of both inflammatory and apoptotic signaling pathways in the deep hypothermic circulatory arrest group. Nuclear factor-kB, a key driver of inflammation, appears to be an upstream regulator of the majority of the upregulated genes; hence, nuclear factor-kB inhibitors could potentially be tested for beneficial effects on neurologic outcome., (Copyright © 2019. Published by Elsevier Inc.)
- Published
- 2019
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26. The Effect of Mouse Strain, Sex, and Carcinogen Dose on Toxicity and the Development of Lung Dysplasia and Squamous Cell Carcinomas in Mice.
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Riolobos L, Gad EA, Treuting PM, Timms AE, Hershberg EA, Corulli LR, Rodmaker E, and Disis ML
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- Animals, Carcinoma, Squamous Cell chemically induced, Carcinoma, Squamous Cell pathology, Carmustine analogs & derivatives, Carmustine toxicity, Cell Transformation, Neoplastic chemically induced, Dose-Response Relationship, Drug, Female, Incidence, Lung drug effects, Lung Neoplasms chemically induced, Lung Neoplasms pathology, Male, Mice, Neoplasms, Experimental chemically induced, Neoplasms, Experimental epidemiology, Neoplasms, Experimental pathology, Risk Factors, Sex Factors, Carcinogens toxicity, Carcinoma, Squamous Cell epidemiology, Lung pathology, Lung Neoplasms epidemiology
- Abstract
In order to translate new treatments to the clinic, it is necessary to use animal models that closely recapitulate human disease. Lung cancer develops after extended exposure to carcinogens. It has one of the highest mutation rates of all cancer and is highly heterogenic. Topical treatment with N-nitrosotris-(2-chloroethyl)urea (NTCU) induces lung squamous cell carcinoma (SCC) with nonsynonymous mutation rates similar to those reported for human non-small cell lung cancer. However, NTCU induces lung cancer with variable efficacy and toxicity depending on the mouse strain. A detailed characterization of the NTCU model is needed. We have compared the effect of three different NTCU doses (20, 30, and 40 mmol/L) in female and male of NIH Swiss, Black Swiss, and FVB mice on tumor incidence, survival, and toxicity. The main findings in this study are (1) NIH Swiss mice present with a higher incidence of SCC and lower mortality compared with Black Swiss and FVB mice; (2) 30 mmol/L NTCU dose induces SCC at the same rate and incidence as the 40 mmol/L dose with lower mortality; (3) female mice present higher grade and incidence of preinvasive lesions and SCC compared with males; (4) NTCU-induced transformation is principally within the respiratory system; and (5) NTCU treatment does not affect the ability to elicit a specific adaptive immune response. This study provides a reference point for experimental designs to evaluate either preventive or therapeutic treatments for lung SCC, including immunotherapies, before initiating human clinical trials., (©2019 American Association for Cancer Research.)
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- 2019
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27. MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance.
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Dobyns WB, Aldinger KA, Ishak GE, Mirzaa GM, Timms AE, Grout ME, Dremmen MHG, Schot R, Vandervore L, van Slegtenhorst MA, Wilke M, Kasteleijn E, Lee AS, Barry BJ, Chao KR, Szczałuba K, Kobori J, Hanson-Kahn A, Bernstein JA, Carr L, D'Arco F, Miyana K, Okazaki T, Saito Y, Sasaki M, Das S, Wheeler MM, Bamshad MJ, Nickerson DA, Engle EC, Verheijen FW, Doherty D, and Mancini GMS
- Subjects
- Adolescent, Brain Stem pathology, Child, Child, Preschool, Cilia genetics, Female, Humans, Lissencephaly genetics, Male, Microtubules genetics, Nervous System Malformations genetics, Axon Guidance genetics, Cell Movement genetics, Conserved Sequence genetics, Microfilament Proteins genetics, Mutation genetics, Neurons pathology, Zinc metabolism
- Abstract
To date, mutations in 15 actin- or microtubule-associated genes have been associated with the cortical malformation lissencephaly and variable brainstem hypoplasia. During a multicenter review, we recognized a rare lissencephaly variant with a complex brainstem malformation in three unrelated children. We searched our large brain-malformation databases and found another five children with this malformation (as well as one with a less severe variant), analyzed available whole-exome or -genome sequencing data, and tested ciliogenesis in two affected individuals. The brain malformation comprised posterior predominant lissencephaly and midline crossing defects consisting of absent anterior commissure and a striking W-shaped brainstem malformation caused by small or absent pontine crossing fibers. We discovered heterozygous de novo missense variants or an in-frame deletion involving highly conserved zinc-binding residues within the GAR domain of MACF1 in the first eight subjects. We studied cilium formation and found a higher proportion of mutant cells with short cilia than of control cells with short cilia. A ninth child had similar lissencephaly but only subtle brainstem dysplasia associated with a heterozygous de novo missense variant in the spectrin repeat domain of MACF1. Thus, we report variants of the microtubule-binding GAR domain of MACF1 as the cause of a distinctive and most likely pathognomonic brain malformation. A gain-of-function or dominant-negative mechanism appears likely given that many heterozygous mutations leading to protein truncation are included in the ExAC Browser. However, three de novo variants in MACF1 have been observed in large schizophrenia cohorts., (Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
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28. Analysis of 17 genes detects mutations in 81% of 811 patients with lissencephaly.
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Di Donato N, Timms AE, Aldinger KA, Mirzaa GM, Bennett JT, Collins S, Olds C, Mei D, Chiari S, Carvill G, Myers CT, Rivière JB, Zaki MS, Gleeson JG, Rump A, Conti V, Parrini E, Ross ME, Ledbetter DH, Guerrini R, and Dobyns WB
- Subjects
- Brain physiopathology, Classical Lissencephalies and Subcortical Band Heterotopias diagnostic imaging, Classical Lissencephalies and Subcortical Band Heterotopias genetics, Classical Lissencephalies and Subcortical Band Heterotopias physiopathology, DNA Mutational Analysis, Female, Genetic Association Studies, Humans, Lissencephaly diagnostic imaging, Lissencephaly genetics, Lissencephaly physiopathology, Male, Mutation genetics, Reelin Protein, Brain diagnostic imaging, Classical Lissencephalies and Subcortical Band Heterotopias diagnosis, Lissencephaly diagnosis, Exome Sequencing
- Abstract
Purpose: To estimate diagnostic yield and genotype-phenotype correlations in a cohort of 811 patients with lissencephaly or subcortical band heterotopia., Methods: We collected DNA from 756 children with lissencephaly over 30 years. Many were tested for deletion 17p13.3 and mutations of LIS1, DCX, and ARX, but few other genes. Among those tested, 216 remained unsolved and were tested by a targeted panel of 17 genes (ACTB, ACTG1, ARX, CRADD, DCX, LIS1, TUBA1A, TUBA8, TUBB2B, TUBB, TUBB3, TUBG1, KIF2A, KIF5C, DYNC1H1, RELN, and VLDLR) or by whole-exome sequencing. Fifty-five patients studied at another institution were added as a validation cohort., Results: The overall mutation frequency in the entire cohort was 81%. LIS1 accounted for 40% of patients, followed by DCX (23%), TUBA1A (5%), and DYNC1H1 (3%). Other genes accounted for 1% or less of patients. Nineteen percent remained unsolved, which suggests that several additional genes remain to be discovered. The majority of unsolved patients had posterior pachygyria, subcortical band heterotopia, or mild frontal pachygyria., Conclusion: The brain-imaging pattern correlates with mutations in single lissencephaly-associated genes, as well as in biological pathways. We propose the first LIS classification system based on the underlying molecular mechanisms.
- Published
- 2018
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29. Bi-allelic mutations of CCDC88C are a rare cause of severe congenital hydrocephalus.
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Ruggeri G, Timms AE, Cheng C, Weiss A, Kollros P, Chapman T, Tully H, and Mirzaa GM
- Subjects
- Brain abnormalities, Female, Genes, Recessive, Genetic Association Studies, Genotype, Humans, Hydrocephalus therapy, Infant, Magnetic Resonance Imaging, Male, Pedigree, Severity of Illness Index, Exome Sequencing, Alleles, Hydrocephalus diagnosis, Hydrocephalus genetics, Intracellular Signaling Peptides and Proteins genetics, Microfilament Proteins genetics, Mutation, Phenotype
- Abstract
Congenital or infantile hydrocephalus is caused by genetic and non-genetic factors and is highly heterogeneous in etiology. In recent studies, a limited number of genetic causes of hydrocephalus have been identified. To date, recessive mutations in the CCDC88C gene have been identified as a cause of non-syndromic congenital hydrocephalus in three reported families. Here, we report the fourth known family with two affected individuals with congenital hydrocephalus due to a homozygous mutation in the CCDC88C gene identified by whole exome sequencing. Our two newly described children, as well as the previously published ones, all shared several features including severe infantile-onset hydrocephalus, mild to severe intellectual delay, varying degrees of motor delay, and infantile onset seizures. All identified homozygous mutations in CCDC88C abolish the PDZ binding site necessary for proper CCDC88C protein function in the Wnt signaling pathway. Our report further establishes CCDC88C as one of the few known recessive causes of severe prenatal-onset hydrocephalus. Recognition of this syndrome has important diagnostic and genetic implications for families identified in the future., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2018
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30. Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice.
- Author
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Geister KA, Timms AE, and Beier DR
- Subjects
- Alkylating Agents toxicity, Animals, Embryo, Mammalian drug effects, Embryo, Mammalian embryology, Embryo, Mammalian metabolism, Ethylnitrosourea toxicity, Female, Genotype, Male, Mice, Inbred C57BL, Mutagenesis drug effects, Phenotype, Chromosome Mapping methods, Genes, Dominant genetics, Genomics methods, Mutation
- Abstract
Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach's efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers., (Copyright © 2018 Geister et al.)
- Published
- 2018
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31. Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.
- Author
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Alcantara D, Timms AE, Gripp K, Baker L, Park K, Collins S, Cheng C, Stewart F, Mehta SG, Saggar A, Sztriha L, Zombor M, Caluseriu O, Mesterman R, Van Allen MI, Jacquinet A, Ygberg S, Bernstein JA, Wenger AM, Guturu H, Bejerano G, Gomez-Ospina N, Lehman A, Alfei E, Pantaleoni C, Conti V, Guerrini R, Moog U, Graham JM Jr, Hevner R, Dobyns WB, O'Driscoll M, and Mirzaa GM
- Subjects
- Brain diagnostic imaging, Child, Developmental Disabilities diagnostic imaging, Developmental Disabilities pathology, Female, Genetic Association Studies, HEK293 Cells, Humans, Immunoprecipitation, Magnetic Resonance Imaging, Male, Megalencephaly diagnostic imaging, Megalencephaly pathology, Mutagenesis, Site-Directed methods, Phosphatidylinositols metabolism, Transfection, Developmental Disabilities genetics, Megalencephaly genetics, Mutation genetics, Proto-Oncogene Proteins c-akt genetics
- Abstract
Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype-phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors., (© The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2017
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32. Update on the ACTG1-associated Baraitser-Winter cerebrofrontofacial syndrome.
- Author
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Di Donato N, Kuechler A, Vergano S, Heinritz W, Bodurtha J, Merchant SR, Breningstall G, Ladda R, Sell S, Altmüller J, Bögershausen N, Timms AE, Hackmann K, Schrock E, Collins S, Olds C, Rump A, and Dobyns WB
- Subjects
- Biomarkers, Brain pathology, Child, Preschool, DNA Mutational Analysis, Exome, Facies, Female, Genetic Association Studies, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Infant, Magnetic Resonance Imaging, Male, Phenotype, Abnormalities, Multiple diagnosis, Abnormalities, Multiple genetics, Actins genetics, Craniofacial Abnormalities diagnosis, Craniofacial Abnormalities genetics, Mutation, Missense
- Abstract
Baraitser-Winter cerebrofrontofacial syndrome is caused by heterozygous missense mutations in one of the two ubiquitous cytoplasmic actin-encoding genes ACTB and ACTG1. Recently, we characterized the large cohort of 41 patients presenting with this condition. Our series contained 34 patients with mutations in ACTB and only nine with ACTG1 mutations. Here, we report on seven unrelated patients with six mutations in ACTG1-four novel and two previously reported. Only one of seven patients was clinically diagnosed with this disorder and underwent ACTB/ACTG1 targeted sequencing, four patients were screened as a part of the large lissencephaly cohort and two were tested with exome sequencing. Retrospectively, facial features were compatible with the diagnosis but significantly milder than previously reported in four patients, and non-specific in one. The pattern of malformations of cortical development was highly similar in four of six patients with available MRI images and encompassed frontal predominant pachygyria merging with the posterior predominant band heterotopia. Two remaining patients showed mild involvement consistent with bilaterally simplified gyration over the frontal lobes. Taken together, we expand the clinical spectrum of the ACTG1-associated Baraitser-Winter cerebrofrontofacial syndrome demonstrating the mild end of the facial and brain manifestations. © 2016 Wiley Periodicals, Inc., (© 2016 Wiley Periodicals, Inc.)
- Published
- 2016
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33. A novel rasopathy caused by recurrent de novo missense mutations in PPP1CB closely resembles Noonan syndrome with loose anagen hair.
- Author
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Gripp KW, Aldinger KA, Bennett JT, Baker L, Tusi J, Powell-Hamilton N, Stabley D, Sol-Church K, Timms AE, and Dobyns WB
- Subjects
- Brain pathology, Child, Child, Preschool, Dandy-Walker Syndrome diagnosis, Dandy-Walker Syndrome genetics, Diagnostic Imaging, Exome, Facies, Female, Genetic Association Studies, Genetic Testing, High-Throughput Nucleotide Sequencing, Humans, Loose Anagen Hair Syndrome metabolism, Male, Noonan Syndrome metabolism, Phenotype, Young Adult, ras Proteins metabolism, Loose Anagen Hair Syndrome diagnosis, Loose Anagen Hair Syndrome genetics, Mutation, Missense, Noonan Syndrome diagnosis, Noonan Syndrome genetics, Protein Phosphatase 1 genetics
- Abstract
Noonan syndrome is a rasopathy caused by mutations in multiple genes encoding components of the RAS/MAPK pathway. Despite its variable phenotype, limited genotype-phenotype correlations exist. Noonan syndrome with loose anagen hair (NS-LAH) is characterized by its distinctive hair anomalies, developmental differences, and structural brain abnormalities and is caused by a single recurrent missense SHOC2 mutation. SHOC2 forms a complex with protein phosphatase 1 (PP1C). Protein phosphatases counterbalance kinases and control activation of signaling proteins, such as the mitogen-activated protein kinases of the RAS/MAPK pathway. Here we report four patients with de novo missense mutations in protein phosphatase one catalytic subunit beta (PPP1CB), sharing a recognizable phenotype. Three individuals had the recurrent PPP1CB c.146G>C, p.Pro49Arg mutation, the fourth had a c.166G>C, p.Ala56Pro change. All had relative or absolute macrocephaly, low-set and posteriorly angulated ears, and developmental delay. Slow growing and/or sparse hair and/or an unruly hair texture was present in all. Three individuals had feeding difficulties requiring feeding tubes. One of two males had cryptorchidism, another had pectus excavatum. Short stature was present in three. A female with the recurrent mutation had a Dandy-Walker malformation and optic nerve hypoplasia. Mild ventriculomegaly occurred in all, cerebellar tonsillar ectopia was seen in two and progressed to Chiari 1 malformation in one individual. Based on the combination of phenotypic findings and PPP1CB's effect on RAF dephosphorylation within the RAS/MAPK pathway, this novel condition can be considered a rasopathy, most similar to NS-LAH. Collectively, these mutations meet the standardized criteria for pathogenicity. © 2016 Wiley Periodicals, Inc., Competing Interests: The authors declare no conflict of interest., (© 2016 Wiley Periodicals, Inc.)
- Published
- 2016
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34. Mutations in Dnaaf1 and Lrrc48 Cause Hydrocephalus, Laterality Defects, and Sinusitis in Mice.
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Ha S, Lindsay AM, Timms AE, and Beier DR
- Subjects
- Animals, Animals, Newborn, Cilia genetics, Female, Functional Laterality genetics, Infertility, Male genetics, Male, Mice, Mutant Strains, Hydrocephalus genetics, Microtubule-Associated Proteins genetics, Mutation, Sinusitis genetics
- Abstract
We have previously described a forward genetic screen in mice for abnormalities of brain development. Characterization of two hydrocephalus mutants by whole-exome sequencing after whole-genome SNP mapping revealed novel recessive mutations in Dnaaf1 and Lrrc48 Mouse mutants of these two genes have not been previously reported. The Dnaaf1 mutant carries a mutation at the splice donor site of exon 4, which results in abnormal transcripts. The Lrrc48 mutation is a missense mutation at a highly conserved leucine residue, which is also associated with a decrease in Lrrc48 transcription. Both Dnaaf1 and Lrrc48 belong to a leucine-rich repeat-containing protein family and are components of the ciliary axoneme. Their Chlamydomonas orthologs are known to be required for normal ciliary beat frequency or flagellar waveform, respectively. Some Dnaaf1 or Lrrc48 homozygote mutants displayed laterality defects, suggesting a motile cilia defect in the embryonic node. Mucus accumulation and neutrophil infiltration in the maxillary sinuses suggested sinusitis. Dnaaf1 mutants showed postnatal lethality, and none survived to weaning age. Lrrc48 mutants survive to adulthood, but had male infertility. ARL13B immunostaining showed the presence of motile cilia in the mutants, and the distal distribution of DNAH9 in the axoneme of upper airway motile cilia appeared normal. The phenotypic abnormalities suggest that mutations in Dnaaf1 and Lrrc48 cause defects in motile cilia function., (Copyright © 2016 Ha et al.)
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- 2016
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35. Improvement of ENU Mutagenesis Efficiency Using Serial Injection and Mismatch Repair Deficiency Mice.
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Gallego-Llamas J, Timms AE, Pitstick R, Peters J, Carlson GA, and Beier DR
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- Animals, Base Pairing genetics, Breeding, Female, Fertility, Mice, Inbred C57BL, Mice, Inbred ICR, Mutation genetics, Survival Analysis, DNA Mismatch Repair genetics, Ethylnitrosourea chemistry, Mutagenesis genetics
- Abstract
ENU mutagenesis is a powerful method for generating novel lines of mice that are informative with respect to both fundamental biological processes and human disease. Rapid developments in genomic technology have made the task of identifying causal mutations by positional cloning remarkably efficient. One limitation of this approach remains the mutation frequency achievable using standard treatment protocols, which currently generate approximately 1-2 sequence changes per megabase when optimized. In this study we used two strategies to attempt to increase the number of mutations induced by ENU treatment. One approach employed mice carrying a mutation in the DNA repair enzyme Msh6. The second strategy involved injection of ENU to successive generations of mice. To evaluate the number of ENU-induced mutations, single mice or pooled samples were analyzed using whole exome sequencing. The results showed that there is considerable variability in the induced mutation frequency using these approaches, but an overall increase in ENU-induced variants from one generation to another was observed. The analysis of the mice deficient for Msh6 also showed an increase in the ENU-induced variants compared to the wild-type ENU-treated mice. However, in both cases the increase in ENU-induced mutation frequency was modest.
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- 2016
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36. Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism.
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Mirzaa GM, Campbell CD, Solovieff N, Goold C, Jansen LA, Menon S, Timms AE, Conti V, Biag JD, Adams C, Boyle EA, Collins S, Ishak G, Poliachik S, Girisha KM, Yeung KS, Chung BHY, Rahikkala E, Gunter SA, McDaniel SS, Macmurdo CF, Bernstein JA, Martin B, Leary R, Mahan S, Liu S, Weaver M, Doerschner M, Jhangiani S, Muzny DM, Boerwinkle E, Gibbs RA, Lupski JR, Shendure J, Saneto RP, Novotny EJ, Wilson CJ, Sellers WR, Morrissey M, Hevner RF, Ojemann JG, Guerrini R, Murphy LO, Winckler W, and Dobyns WB
- Subjects
- Adolescent, Adult, Amino Acids pharmacology, Animals, Cells, Cultured, Cerebral Cortex cytology, Child, Child, Preschool, Developmental Disabilities diagnostic imaging, Developmental Disabilities genetics, Embryo, Mammalian, Female, Gene Expression Regulation drug effects, Gene Expression Regulation genetics, Genetic Association Studies, Humans, Intercellular Signaling Peptides and Proteins deficiency, Male, Malformations of Cortical Development diagnostic imaging, Mechanistic Target of Rapamycin Complex 1, Megalencephaly diagnostic imaging, Multiprotein Complexes pharmacology, Nerve Tissue Proteins genetics, Nerve Tissue Proteins metabolism, Neurons drug effects, Rats, Retrospective Studies, TOR Serine-Threonine Kinases metabolism, TOR Serine-Threonine Kinases pharmacology, Young Adult, Malformations of Cortical Development genetics, Megalencephaly genetics, Mosaicism, Mutation genetics, TOR Serine-Threonine Kinases genetics
- Abstract
Importance: Focal cortical dysplasia (FCD), hemimegalencephaly, and megalencephaly constitute a spectrum of malformations of cortical development with shared neuropathologic features. These disorders are associated with significant childhood morbidity and mortality., Objective: To identify the underlying molecular cause of FCD, hemimegalencephaly, and diffuse megalencephaly., Design, Setting, and Participants: Patients with FCD, hemimegalencephaly, or megalencephaly (mean age, 11.7 years; range, 2-32 years) were recruited from Pediatric Hospital A. Meyer, the University of Hong Kong, and Seattle Children's Research Institute from June 2012 to June 2014. Whole-exome sequencing (WES) was performed on 8 children with FCD or hemimegalencephaly using standard-depth (50-60X) sequencing in peripheral samples (blood, saliva, or skin) from the affected child and their parents and deep (150-180X) sequencing in affected brain tissue. Targeted sequencing and WES were used to screen 93 children with molecularly unexplained diffuse or focal brain overgrowth. Histopathologic and functional assays of phosphatidylinositol 3-kinase-AKT (serine/threonine kinase)-mammalian target of rapamycin (mTOR) pathway activity in resected brain tissue and cultured neurons were performed to validate mutations., Main Outcomes and Measures: Whole-exome sequencing and targeted sequencing identified variants associated with this spectrum of developmental brain disorders., Results: Low-level mosaic mutations of MTOR were identified in brain tissue in 4 children with FCD type 2a with alternative allele fractions ranging from 0.012 to 0.086. Intermediate-level mosaic mutation of MTOR (p.Thr1977Ile) was also identified in 3 unrelated children with diffuse megalencephaly and pigmentary mosaicism in skin. Finally, a constitutional de novo mutation of MTOR (p.Glu1799Lys) was identified in 3 unrelated children with diffuse megalencephaly and intellectual disability. Molecular and functional analysis in 2 children with FCD2a from whom multiple affected brain tissue samples were available revealed a mutation gradient with an epicenter in the most epileptogenic area. When expressed in cultured neurons, all MTOR mutations identified here drive constitutive activation of mTOR complex 1 and enlarged neuronal size., Conclusions and Relevance: In this study, mutations of MTOR were associated with a spectrum of brain overgrowth phenotypes extending from FCD type 2a to diffuse megalencephaly, distinguished by different mutations and levels of mosaicism. These mutations may be sufficient to cause cellular hypertrophy in cultured neurons and may provide a demonstration of the pattern of mosaicism in brain and substantiate the link between mosaic mutations of MTOR and pigmentary mosaicism in skin.
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- 2016
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37. PIK3CA -associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution.
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Mirzaa G, Timms AE, Conti V, Boyle EA, Girisha KM, Martin B, Kircher M, Olds C, Juusola J, Collins S, Park K, Carter M, Glass I, Krägeloh-Mann I, Chitayat D, Parikh AS, Bradshaw R, Torti E, Braddock S, Burke L, Ghedia S, Stephan M, Stewart F, Prasad C, Napier M, Saitta S, Straussberg R, Gabbett M, O'Connor BC, Keegan CE, Yin LJ, Lai AHM, Martin N, McKinnon M, Addor MC, Boccuto L, Schwartz CE, Lanoel A, Conway RL, Devriendt K, Tatton-Brown K, Pierpont ME, Painter M, Worgan L, Reggin J, Hennekam R, Tsuchiya K, Pritchard CC, Aracena M, Gripp KW, Cordisco M, Van Esch H, Garavelli L, Curry C, Goriely A, Kayserilli H, Shendure J, Graham J Jr, Guerrini R, and Dobyns WB
- Subjects
- Female, Genetic Association Studies, High-Throughput Nucleotide Sequencing, Humans, Infant, Male, Mutation, Phenotype, Tissue Distribution, Class I Phosphatidylinositol 3-Kinases genetics, Malformations of Cortical Development genetics, Mosaicism, Vascular Malformations genetics
- Abstract
Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals ( n = 12) were identified separately to have mutations in PIK3CA by clinical targeted-panel testing ( n = 6), whole-exome sequencing ( n = 5), or Sanger sequencing ( n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA -related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations.
- Published
- 2016
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38. Mosaic Activating Mutations in FGFR1 Cause Encephalocraniocutaneous Lipomatosis.
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Bennett JT, Tan TY, Alcantara D, Tétrault M, Timms AE, Jensen D, Collins S, Nowaczyk MJM, Lindhurst MJ, Christensen KM, Braddock SR, Brandling-Bennett H, Hennekam RCM, Chung B, Lehman A, Su J, Ng S, Amor DJ, Majewski J, Biesecker LG, Boycott KM, Dobyns WB, O'Driscoll M, Moog U, and McDonell LM
- Subjects
- Adolescent, Cell Line, Tumor, Central Nervous System Neoplasms diagnosis, Central Nervous System Neoplasms genetics, Child, Preschool, Exome, Eye physiopathology, Eye Diseases diagnosis, Female, Humans, Infant, Lipomatosis diagnosis, Male, Mutation, Mutation, Missense, Neurocutaneous Syndromes diagnosis, Phosphatidylinositol 3-Kinases genetics, Phosphatidylinositol 3-Kinases metabolism, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism, Receptor, Fibroblast Growth Factor, Type 1 metabolism, Seizures genetics, Sequence Analysis, DNA, Eye Diseases genetics, Lipomatosis genetics, Neurocutaneous Syndromes genetics, Receptor, Fibroblast Growth Factor, Type 1 genetics
- Abstract
Encephalocraniocutaneous lipomatosis (ECCL) is a sporadic condition characterized by ocular, cutaneous, and central nervous system anomalies. Key clinical features include a well-demarcated hairless fatty nevus on the scalp, benign ocular tumors, and central nervous system lipomas. Seizures, spasticity, and intellectual disability can be present, although affected individuals without seizures and with normal intellect have also been reported. Given the patchy and asymmetric nature of the malformations, ECCL has been hypothesized to be due to a post-zygotic, mosaic mutation. Despite phenotypic overlap with several other disorders associated with mutations in the RAS-MAPK and PI3K-AKT pathways, the molecular etiology of ECCL remains unknown. Using exome sequencing of DNA from multiple affected tissues from five unrelated individuals with ECCL, we identified two mosaic mutations, c.1638C>A (p.Asn546Lys) and c.1966A>G (p.Lys656Glu) within the tyrosine kinase domain of FGFR1, in two affected individuals each. These two residues are the most commonly mutated residues in FGFR1 in human cancers and are associated primarily with CNS tumors. Targeted resequencing of FGFR1 in multiple tissues from an independent cohort of individuals with ECCL identified one additional individual with a c.1638C>A (p.Asn546Lys) mutation in FGFR1. Functional studies of ECCL fibroblast cell lines show increased levels of phosphorylated FGFRs and phosphorylated FRS2, a direct substrate of FGFR1, as well as constitutive activation of RAS-MAPK signaling. In addition to identifying the molecular etiology of ECCL, our results support the emerging overlap between mosaic developmental disorders and tumorigenesis., (Copyright © 2016 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
- Published
- 2016
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39. Erratum: Heritable GATA2 mutations associated with familial AML-MDS: a case report and review of literature.
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Gao J, Gentzler RD, Timms AE, Horwitz MS, Frankfurt O, Altman JK, and Peterson LC
- Published
- 2015
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40. Characterisation of mutations of the phosphoinositide-3-kinase regulatory subunit, PIK3R2, in perisylvian polymicrogyria: a next-generation sequencing study.
- Author
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Mirzaa GM, Conti V, Timms AE, Smyser CD, Ahmed S, Carter M, Barnett S, Hufnagel RB, Goldstein A, Narumi-Kishimoto Y, Olds C, Collins S, Johnston K, Deleuze JF, Nitschké P, Friend K, Harris C, Goetsch A, Martin B, Boyle EA, Parrini E, Mei D, Tattini L, Slavotinek A, Blair E, Barnett C, Shendure J, Chelly J, Dobyns WB, and Guerrini R
- Subjects
- Adolescent, Child, Child, Preschool, DNA Mutational Analysis, Humans, Infant, Young Adult, Abnormalities, Multiple genetics, Intellectual Disability genetics, Malformations of Cortical Development genetics, Mutation, Phosphatidylinositol 3-Kinases genetics
- Abstract
Background: Bilateral perisylvian polymicrogyria (BPP), the most common form of regional polymicrogyria, causes the congenital bilateral perisylvian syndrome, featuring oromotor dysfunction, cognitive impairment, and epilepsy. The causes of BPP are heterogeneous, but only a few genetic causes have been reported. The aim of this study was to identify additional genetic causes of BPP and characterise their frequency in this population., Methods: Children (aged ≤18 years) with polymicrogyria were enrolled into our research programme from July, 1980, to October, 2015, at two centres (Florence, Italy, and Seattle, WA, USA). We obtained samples (blood and saliva) throughout this period at both centres and did whole-exome sequencing on DNA from eight trios (two parents and one affected child) with BPP in 2014. After the identification of mosaic PIK3R2 mutations in two of these eight children, we performed targeted screening of PIK3R2 by two methods in a cohort of 118 children with BPP. First, we performed targeted sequencing of the entire PIK3R2 gene by single molecule molecular inversion probes (smMIPs) on 38 patients with BPP with normal to large head size. Second, we did amplicon sequencing of the recurrent PIK3R2 mutation (Gly373Arg) in 80 children with various types of polymicrogyria including BPP. One additional patient had clinical whole-exome sequencing done independently, and was included in this study because of the phenotypic similarity to our cohort., Findings: We identified a mosaic mutation (Gly373Arg) in a regulatory subunit of the PI3K-AKT-mTOR pathway, PIK3R2, in two children with BPP. Of the 38 patients with BPP and normal to large head size who underwent targeted next-generation sequencing by smMIPs, we identified constitutional and mosaic PIK3R2 mutations in 17 additional children. In parallel, one patient had the recurrent PIK3R2 mutation identified by clinical whole-exome sequencing. Seven of these 20 patients had BPP alone, and 13 had BPP in association with features of the megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH) syndrome. 19 patients had the same mutation (Gly373Arg), and one had a nearby missense mutation (Lys376Glu). Mutations were constitutional in 12 patients and mosaic in eight patients. In patients with mosaic mutations, we noted substantial variation in alternate (mutant) allele levels, ranging from ten (3%) of 377 reads to 39 (37%) of 106 reads, equivalent to 5-73% of cells analysed. Levels of mosaicism varied from undetectable to 37 (17%) of 216 reads in blood-derived DNA compared with 2030 (29%) of 6889 reads to 275 (43%) of 634 reads in saliva-derived DNA., Interpretation: Constitutional and mosaic mutations in the PIK3R2 gene are associated with developmental brain disorders ranging from BPP with a normal head size to the MPPH syndrome. The phenotypic variability and low-level mosaicism, which challenge conventional molecular methods, have important implications for genetic testing and counselling., Funding: US National Institutes of Health., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2015
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41. Variant mapping and mutation discovery in inbred mice using next-generation sequencing.
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Gallego-Llamas J, Timms AE, Geister KA, Lindsay A, and Beier DR
- Subjects
- Animals, Exome genetics, Female, Male, Mice, Mutation genetics, Pedigree, High-Throughput Nucleotide Sequencing methods
- Abstract
Background: The development of powerful new methods for DNA sequencing enable the discovery of sequence variants, their utilization for the mapping of mutant loci, and the identification of causal variants in a single step. We have applied this approach for the analysis of ENU-mutagenized mice maintained on an inbred background., Results: We ascertained ENU-induced variants in four different phenotypically mutant lines. These were then used as informative markers for positional cloning of the mutated genes. We tested both whole genome (WGS) and whole exome (WES) datasets., Conclusion: Both approaches were successful as a means to localize a region of homozygosity, as well as identifying mutations of candidate genes, which could be individually assessed. As expected, the WGS strategy was more reliable, since many more ENU-induced variants were ascertained.
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- 2015
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42. Osteoblast differentiation profiles define sex specific gene expression patterns in craniosynostosis.
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Park SS, Beyer RP, Smyth MD, Clarke CM, Timms AE, Bammler TK, Stamper BD, Mecham BH, Gustafson JA, and Cunningham ML
- Subjects
- Cell Proliferation, Cells, Cultured, Craniosynostoses pathology, Female, Humans, Male, Osteoblasts metabolism, Cell Differentiation, Craniosynostoses genetics, Gene Expression Profiling, Osteoblasts pathology, Sex Factors
- Abstract
Single suture craniosynostosis (SSC) is the premature fusion of one calvarial suture and occurs in 1-1700-2500 live births. Congenital fusion of either the sagittal, metopic, or coronal sutures represents 95% of all cases of SSC. Sagittal and metopic synostosis have a male preponderance (3:1) while premature fusion of the coronal suture has a female preponderance (2:1). Although environmental and genetic factors contribute to SSC, the etiology of the majority of SSC cases remains unclear. In this study, 227 primary calvarial osteoblast cell lines from patients with coronal, metopic, or sagittal synostosis and unaffected controls were established and assayed for ALP activity and BrdU incorporation (n = 226) as respective measures of early stage osteoblast differentiation and proliferation. Primary osteoblast cell lines from individuals with sagittal synostosis demonstrated higher levels of ALP activity and reduced proliferation when compared to control lines. In order to address the sex differences in SSC types, the data was further stratified by sex. Osteoblasts from males and females with sagittal synostosis as well as males with metopic synostosis demonstrated higher levels of ALP activity when compared to sex matched controls, and males with sagittal or metopic synostosis demonstrated reduced levels of proliferation. In order to elucidate genes and pathways involved in these observed phenotypes, correlation analyses comparing ALP activity and proliferation to global gene expression was performed. Transcripts related to osteoblast differentiation were identified both differentially up and downregulated, correlated with ALP activity when compared to controls, and demonstrated a striking sex specific gene expression pattern. These data support that the dysregulation of osteoblast differentiation plays a role in the development of SSC and that genetic factors contribute to the observed sex related differences., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2015
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43. Heritable GATA2 mutations associated with familial AML-MDS: a case report and review of literature.
- Author
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Gao J, Gentzler RD, Timms AE, Horwitz MS, Frankfurt O, Altman JK, and Peterson LC
- Subjects
- Acute Disease, Base Sequence, DNA Mutational Analysis, Family Health, Female, Heterozygote, Humans, Karyotyping, Middle Aged, GATA2 Transcription Factor genetics, Leukemia, Myeloid genetics, Mutation, Missense, Myelodysplastic Syndromes genetics
- Abstract
A 50-year-old woman was diagnosed with acute myeloid leukemia (AML). She has history of thrombocytopenia for 25 years and a significant family history of thrombocytopenia, affecting her mother, siblings and their children, as well as her own children. Both her mother and maternal aunt died from myelodysplastic syndrome (MDS). Additional genetic analysis was performed and identified two heterozygous missence mutations in the second zinc finger domain of GATA2 gene (p.Thr358Lys, and p.Leu359Val), occurring in cis on the same allele. Given the patient's family history and clinical manifestation, this was interpreted as an acute myeloid leukemia with heritable GATA2 mutations associated with familial AML-MDS. Germline GATA2 mutations are involved in a group of complex syndromes with overlapping clinical features of immune deficiency, lymphedema and propensity to acute myeloid leukemia or myelodysplastic syndrome (AML-MDS). Here we reported a case of familial AML-MDS with two novel GATA2 mutations. This case illustrates the importance of recognizing the clinical features for this rare category of AML-MDS and performing the appropriate molecular testing. The diagnosis of heritable gene mutations associated familial AML-MDS has significant clinical implication for the patients and affected families. Clinical trials are available to further investigate the role of allogeneic hematopoietic stem cell transplant in managing these patients.
- Published
- 2014
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44. A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia.
- Author
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Shah S, Schrader KA, Waanders E, Timms AE, Vijai J, Miething C, Wechsler J, Yang J, Hayes J, Klein RJ, Zhang J, Wei L, Wu G, Rusch M, Nagahawatte P, Ma J, Chen SC, Song G, Cheng J, Meyers P, Bhojwani D, Jhanwar S, Maslak P, Fleisher M, Littman J, Offit L, Rau-Murthy R, Fleischut MH, Corines M, Murali R, Gao X, Manschreck C, Kitzing T, Murty VV, Raimondi S, Kuiper RP, Simons A, Schiffman JD, Onel K, Plon SE, Wheeler D, Ritter D, Ziegler DS, Tucker K, Sutton R, Chenevix-Trench G, Li J, Huntsman DG, Hansford S, Senz J, Walsh T, Lee M, Hahn CN, Roberts K, King MC, Lo SM, Levine RL, Viale A, Socci ND, Nathanson KL, Scott HS, Daly M, Lipkin SM, Lowe SW, Downing JR, Altshuler D, Sandlund JT, Horwitz MS, Mullighan CG, and Offit K
- Subjects
- Humans, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease, Germ-Line Mutation, PAX5 Transcription Factor genetics, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma genetics
- Abstract
Somatic alterations of the lymphoid transcription factor gene PAX5 (also known as BSAP) are a hallmark of B cell precursor acute lymphoblastic leukemia (B-ALL), but inherited mutations of PAX5 have not previously been described. Here we report a new heterozygous germline variant, c.547G>A (p.Gly183Ser), affecting the octapeptide domain of PAX5 that was found to segregate with disease in two unrelated kindreds with autosomal dominant B-ALL. Leukemic cells from all affected individuals in both families exhibited 9p deletion, with loss of heterozygosity and retention of the mutant PAX5 allele at 9p13. Two additional sporadic ALL cases with 9p loss harbored somatic PAX5 substitutions affecting Gly183. Functional and gene expression analysis of the PAX5 mutation demonstrated that it had significantly reduced transcriptional activity. These data extend the role of PAX5 alterations in the pathogenesis of pre-B cell ALL and implicate PAX5 in a new syndrome of susceptibility to pre-B cell neoplasia.
- Published
- 2013
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45. Support for the N-methyl-D-aspartate receptor hypofunction hypothesis of schizophrenia from exome sequencing in multiplex families.
- Author
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Timms AE, Dorschner MO, Wechsler J, Choi KY, Kirkwood R, Girirajan S, Baker C, Eichler EE, Korvatska O, Roche KW, Horwitz MS, and Tsuang DW
- Subjects
- Comparative Genomic Hybridization methods, DNA Copy Number Variations genetics, Exome genetics, Family, Female, Genetic Linkage genetics, Genetic Loci genetics, Genome-Wide Association Study methods, Haplotypes genetics, Humans, Male, Models, Biological, Pedigree, Receptor, Metabotropic Glutamate 5, Receptors, Metabotropic Glutamate genetics, Receptors, Metabotropic Glutamate physiology, Receptors, N-Methyl-D-Aspartate physiology, Risk Factors, Receptors, N-Methyl-D-Aspartate genetics, Schizophrenia genetics
- Abstract
Importance: Schizophrenia is a complex genetic disorder demonstrating considerable heritability. Genetic studies have implicated many different genes and pathways, but much of the genetic liability remains unaccounted for. Investigation of genetic forms of schizophrenia will lead to a better understanding of the underlying molecular pathways, which will then enable targeted approaches for disease prevention and treatment., Objective: To identify new genetic factors strongly predisposing to schizophrenia in families with multiple affected individuals with schizophrenia., Design: We performed genome-wide array comparative genomic hybridization, linkage analysis, and exome sequencing in multiplex families with schizophrenia., Setting: Probands and their family members were recruited from academic medical centers., Participants: We intended to identify rare disease-causing mutations in 5 large families where schizophrenia transmission appears consistent with single-gene inheritance., Intervention: Array comparative genomic hybridization was used to identify copy number variants, while exome sequencing was used to identify variants shared in all affected individuals and linkage analysis was used to further filter shared variants of interest. Analysis of select variants was performed in cultured cells to assess their functional consequences., Main Outcome Measures: Rare inherited disease-related genetic mutations., Results: No segregating rare copy number variants were detected by array comparative genomic hybridization. However, in all 5 families, exome sequencing detected rare protein-altering variants in 1 of 3 genes associated with the N -methyl-D-aspartate (NMDA) receptor. One pedigree shared a missense and frameshift substitution of GRM5, encoding the metabotropic glutamate receptor subtype 5 (mGluR5), which is coupled to the NMDA receptor and potentiates its signaling; the frameshift disrupts binding to the scaffolding protein tamalin and increases mGluR5 internalization. Another pedigree transmitted a missense substitution in PPEF2, encoding a calmodulin-binding protein phosphatase, which we show influences mGluR5 levels. Three pedigrees demonstrated different missense substitutions within LRP1B, encoding a low-density lipoprotein receptor-related protein tied to both the NMDA receptor and located in a chromosome 2q22 region previously strongly linked to schizophrenia., Conclusions and Relevance: Exome sequencing of multiplex pedigrees uncovers new genes associated with risk for developing schizophrenia and suggests potential novel therapeutic targets.
- Published
- 2013
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46. Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia.
- Author
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Hahn CN, Chong CE, Carmichael CL, Wilkins EJ, Brautigan PJ, Li XC, Babic M, Lin M, Carmagnac A, Lee YK, Kok CH, Gagliardi L, Friend KL, Ekert PG, Butcher CM, Brown AL, Lewis ID, To LB, Timms AE, Storek J, Moore S, Altree M, Escher R, Bardy PG, Suthers GK, D'Andrea RJ, Horwitz MS, and Scott HS
- Subjects
- Amino Acid Sequence, Animals, COS Cells, Cell Differentiation, Cell Proliferation, Chlorocebus aethiops, Chromosome Mapping, DNA, Complementary, Female, GATA2 Transcription Factor metabolism, Genetic Predisposition to Disease, HEK293 Cells, Haplotypes, Humans, Male, Molecular Sequence Data, Pedigree, Plasmids, Polymorphism, Single Nucleotide, GATA2 Transcription Factor genetics, Leukemia, Myeloid, Acute genetics, Mutation, Myelodysplastic Syndromes genetics, Quantitative Trait, Heritable
- Abstract
We report the discovery of GATA2 as a new myelodysplastic syndrome (MDS)-acute myeloid leukemia (AML) predisposition gene. We found the same, previously unidentified heterozygous c.1061C>T (p.Thr354Met) missense mutation in the GATA2 transcription factor gene segregating with the multigenerational transmission of MDS-AML in three families and a GATA2 c.1063_1065delACA (p.Thr355del) mutation at an adjacent codon in a fourth MDS family. The resulting alterations reside within the second zinc finger of GATA2, which mediates DNA-binding and protein-protein interactions. We show differential effects of the mutations on the transactivation of target genes, cellular differentiation, apoptosis and global gene expression. Identification of such predisposing genes to familial forms of MDS and AML is critical for more effective diagnosis and prognosis, counseling, selection of related bone marrow transplant donors and development of therapies.
- Published
- 2011
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47. KLHDC8B in Hodgkin lymphoma and possibly twinning.
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Timms AE and Horwitz MS
- Abstract
A key feature of Hodgkin lymphoma is that the malignant cells are binucleated, as a consequence of failed cytokinesis. We recently ascertained a family in which multiple cases of Hodgkin lymphoma had occurred among individuals who inherited a balanced chromosomal translocation. We cloned the translocation breakpoints and found that it disrupted a previously uncharacterized gene, KLHDC8B, encoding a Kelch family protein whose deficiency impairs cytokinesis and leads to binucleated cells. In other families we found a rare single nucleotide polymorphism affecting mitotic translation of KLHDC8B that was associated with and linked to Hodgkin lymphoma. Interestingly, the index family demonstrated an unusual frequency of twins, and there is a previously reported association between Hodgkin lymphoma and twins. Here we review the unusual genetic features of Hodgkin lymphoma, including gender concordance among siblings, and genetically test the hypothesis that KLHDC8B may participate in twinning by disrupting cytokinesis through impediment of polar body separation from oocytes.
- Published
- 2010
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48. Prospective meta-analysis of interleukin 1 gene complex polymorphisms confirms associations with ankylosing spondylitis.
- Author
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Sims AM, Timms AE, Bruges-Armas J, Burgos-Vargas R, Chou CT, Doan T, Dowling A, Fialho RN, Gergely P, Gladman DD, Inman R, Kauppi M, Kaarela K, Laiho K, Maksymowych W, Pointon JJ, Rahman P, Reveille JD, Sorrentino R, Tuomilehto J, Vargas-Alarcon G, Wordsworth BP, Xu H, and Brown MA
- Subjects
- Gene Frequency, Genetic Predisposition to Disease, Genotype, Humans, Interleukin-1alpha genetics, Multigene Family, Prospective Studies, Spondylitis, Ankylosing immunology, Interleukin-1 genetics, Polymorphism, Single Nucleotide, Spondylitis, Ankylosing genetics
- Abstract
Objectives: The aim of the current study was to determine the contribution of interleukin (IL)1 gene cluster polymorphisms previously implicated in susceptibility for ankylosing spondylitis (AS) to AS susceptibility in different populations worldwide., Methods: Nine polymorphisms in the IL1 gene cluster members IL1A (rs2856836, rs17561 and rs1894399), IL1B (rs16944), IL1F10 (rs3811058) and IL1RN (rs419598, the IL1RA VNTR, rs315952 and rs315951) were genotyped in 2675 AS cases and 2592 healthy controls recruited in 12 different centres in 10 countries. Association of variants with AS was tested by Mantel-Haenszel random effects analysis., Results: Strong association was observed with three single nucleotide polymorphisms (SNPs) in the IL1A gene (rs2856836, rs17561, rs1894399, p = 0.0036, 0.000019 and 0.0003, respectively). There was no evidence of significant heterogeneity of effects between centres, and no evidence of non-combinability of findings. The population attributable risk fraction of these variants in Caucasians is estimated at 4-6%., Conclusions: This study confirms that IL1A is associated with susceptibility to AS. Association of the other IL1 gene complex members could not be excluded in specific populations. Prospective meta-analysis is a useful tool in confirmation studies of genes associated with complex genetic disorders such as AS, providing sufficiently large sample sizes to produce robust findings often not achieved in smaller individual cohorts.
- Published
- 2008
- Full Text
- View/download PDF
49. Combined analysis of three whole genome linkage scans for Ankylosing Spondylitis.
- Author
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Carter KW, Pluzhnikov A, Timms AE, Miceli-Richard C, Bourgain C, Wordsworth BP, Jean-Pierre H, Cox NJ, Palmer LJ, Breban M, Reveille JD, and Brown MA
- Subjects
- Chromosomes, Human, Pair 2 genetics, Chromosomes, Human, Pair 22 genetics, Female, Genetic Predisposition to Disease, Genome, Human, Humans, Male, Retrospective Studies, Genetic Linkage, Spondylitis, Ankylosing genetics
- Abstract
Objective: Ankylosing spondylitis (AS) is a debilitating chronic inflammatory condition with a high degree of familiality (lambda(s) = 82) and heritability (>90%) that primarily affects spinal and sacroiliac joints. Whole genome scans for linkage to AS phenotypes have been conducted, although results have been inconsistent between studies and all have had modest sample sizes. One potential solution to these issues is to combine data from multiple studies in a retrospective meta-analysis., Methods: The International Genetics of Ankylosing Spondylitis Consortium combined data from three whole genome linkage scans for AS (n = 3744 subjects) to determine chromosomal markers that show evidence of linkage with disease. Linkage markers typed in different centres were integrated into a consensus map to facilitate effective data pooling. We performed a weighted meta-analysis to combine the linkage results, and compared them with the three individual scans and a combined pooled scan., Results: In addition to the expected region surrounding the HLA-B27 gene on chromosome 6, we determined that several marker regions showed significant evidence of linkage with disease status. Regions on chromosome 10q and 16q achieved 'suggestive' evidence of linkage, and regions on chromosomes 1q, 3q, 5q, 6q, 9q, 17q and 19q showed at least nominal linkage in two or more scans and in the weighted meta-analysis. Regions previously associated with AS on chromosome 2q (the IL-1 gene cluster) and 22q (CYP2D6) exhibited nominal linkage in the meta-analysis, providing further statistical support for their involvement in susceptibility to AS., Conclusion: These findings provide a useful guide for future studies aiming to identify the genes involved in this highly heritable condition.
- Published
- 2007
- Full Text
- View/download PDF
50. Replication of association of IL1 gene complex members with ankylosing spondylitis in Taiwanese Chinese.
- Author
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Chou CT, Timms AE, Wei JC, Tsai WC, Wordsworth BP, and Brown MA
- Subjects
- Case-Control Studies, Chromosomes, Human, Pair 2, Female, Gene Frequency, Genetic Markers, Genotype, Haplotypes, Humans, Linkage Disequilibrium, Male, Spondylitis, Ankylosing ethnology, Taiwan ethnology, Asian People genetics, Interleukin-1 genetics, Polymorphism, Genetic, Spondylitis, Ankylosing genetics
- Abstract
Objective: To test the association of interleukin 1 (IL1) gene family members with ankylosing spondylitis (AS), previously reported in Europid subjects, in an ethnically remote population., Methods: 200 Taiwanese Chinese AS patients and 200 ethnically matched healthy controls were genotyped for five single nucleotide polymorphisms (SNPs) and the IL1RN.VNTR, markers previously associated with AS. Allele, genotype, and haplotype frequencies were compared between cases and controls., Results: Association of alleles and genotypes of the markers IL1F10.3, IL1RN.4, and IL1RN.VNTR was observed with AS (p<0.05). Haplotypes of pairs of these markers and of the markers IL1RN.6/1 and IL1RN.6/2 were also significantly associated with AS. The strongest associations observed were with the marker IL1RN.4, and with the two-marker haplotype IL1RN.4-IL1RN.VNTR (both p = 0.004). Strong linkage disequilibrium was observed between all marker pairs except those involving IL1B-511 (D' 0.4 to 0.9, p<0.01)., Conclusions: The IL1 gene cluster is associated with AS in Taiwanese Chinese. This finding provides strong statistical support that the previously observed association of this gene cluster with AS is a true positive finding. These authors contributed equally to the study.
- Published
- 2006
- Full Text
- View/download PDF
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