Browsing by Author "Wangler, Michael F."

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    Clinical diagnosis of metabolic disorders using untargeted metabolomic profiling and disease-specific networks learned from profiling data
    (Springer Nature, 2022-04-21) Thistlethwaite, Lillian R.; Li, Xiqi; Burrage, Lindsay C.; Riehle, Kevin; Hacia, Joseph G.; Braverman, Nancy; Wangler, Michael F.; Miller, Marcus J.; Elsea, Sarah H.; Milosavljevic, Aleksandar; Medical and Molecular Genetics, School of Medicine
    Untargeted metabolomics is a global molecular profiling technology that can be used to screen for inborn errors of metabolism (IEMs). Metabolite perturbations are evaluated based on current knowledge of specific metabolic pathway deficiencies, a manual diagnostic process that is qualitative, has limited scalability, and is not equipped to learn from accumulating clinical data. Our purpose was to improve upon manual diagnosis of IEMs in the clinic by developing novel computational methods for analyzing untargeted metabolomics data. We employed CTD, an automated computational diagnostic method that "connects the dots" between metabolite perturbations observed in individual metabolomics profiling data and modules identified in disease-specific metabolite co-perturbation networks learned from prior profiling data. We also extended CTD to calculate distances between any two individuals (CTDncd) and between an individual and a disease state (CTDdm), to provide additional network-quantified predictors for use in diagnosis. We show that across 539 plasma samples, CTD-based network-quantified measures can reproduce accurate diagnosis of 16 different IEMs, including adenylosuccinase deficiency, argininemia, argininosuccinic aciduria, aromatic L-amino acid decarboxylase deficiency, cerebral creatine deficiency syndrome type 2, citrullinemia, cobalamin biosynthesis defect, GABA-transaminase deficiency, glutaric acidemia type 1, maple syrup urine disease, methylmalonic aciduria, ornithine transcarbamylase deficiency, phenylketonuria, propionic acidemia, rhizomelic chondrodysplasia punctata, and the Zellweger spectrum disorders. Our approach can be used to supplement information from biochemical pathways and has the potential to significantly enhance the interpretation of variants of uncertain significance uncovered by exome sequencing. CTD, CTDdm, and CTDncd can serve as an essential toolset for biological interpretation of untargeted metabolomics data that overcomes limitations associated with manual diagnosis to assist diagnosticians in clinical decision-making. By automating and quantifying the interpretation of perturbation patterns, CTD can improve the speed and confidence by which clinical laboratory directors make diagnostic and treatment decisions, while automatically improving performance with new case data.
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    Correction: Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype–phenotype correlation
    (Elsevier, 2019-03) Koczkowska, Magdalena; Callens, Tom; Gomes, Alicia; Sharp, Angela; Chen, Yunjia; Hicks, Alesha D.; Aylsworth, Arthur S.; Azizi, Amedeo A.; Basel, Donald G.; Bellus, Gary; Bird, Lynne M.; Blazo, Maria A.; Burke, Leah W.; Cannon, Ashley; Collins, Felicity; DeFilippo, Colette; Denayer, Ellen; Digilio, Maria C.; Dills, Shelley K.; Dosa, Laura; Greenwood, Robert S.; Griffis, Cristin; Gupta, Punita; Hachen, Rachel K.; Hernández-Chico, Concepción; Janssens, Sandra; Jones, Kristi J.; Jordan, Justin T.; Kannu, Peter; Korf, Bruce R.; Lewis, Andrea M.; Listernick, Robert H.; Lonardo, Fortunato; Mahoney, Maurice J.; Ojeda, Mayra Martinez; McDonald, Marie T.; McDougall, Carey; Mendelsohn, Nancy; Miller, David T.; Mori, Mari; Oostenbrink, Rianne; Perreault, Sebastién; Pierpont, Mary Ella; Piscopo, Carmelo; Pond, Dinel A.; Randolph, Linda M.; Rauen, Katherine A.; Rednam, Surya; Rutledge, S. Lane; Saletti, Veronica; Schaefer, G. Bradley; Schorry, Elizabeth K.; Scott, Daryl A.; Shugar, Andrea; Siqveland, Elizabeth; Starr, Lois J.; Syed, Ashraf; Trapane, Pamela L.; Ullrich, Nicole J.; Wakefield, Emily G.; Walsh, Laurence E.; Wangler, Michael F.; Zackai, Elaine; Claes, Kathleen B.M.; Wimmer, Katharina; van Minkelen, Rick; De Luca, Alessandro; Martin, Yolanda; Legius, Eric; Messiaen, Ludwine M.; Neurology, School of Medicine
    Purpose: Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. Methods: A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. Results: None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofi- bromas. We did not identify any complications, such as sympto-matic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_2972del. Conclusion: We demonstrate that individuals with the NF1 p.Met992del pathogenic variant have a mild NF1 phenotype lacking clinically suspected plexiform, cutaneous, or subcutaneous neurofi-bromas. However, learning difficulties are clearly part of the phenotypic presentation in these individuals and will require specialized care.
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    Dicarboxylic acylcarnitine biomarkers in peroxisome biogenesis disorders
    (Elsevier, 2023) Wangler, Michael F.; Lesko, Barbara; Dahal, Rejwi; Jangam, Sharayu; Bhadane, Pradnya; Wilson, Theodore E.; McPheron, Molly; Miller, Marcus J.; Medical and Molecular Genetics, School of Medicine
    The peroxisome is an essential eukaryotic organelle with diverse metabolic functions. Inherited peroxisomal disorders are associated with a wide spectrum of clinical outcomes and are broadly divided into two classes, those impacting peroxisome biogenesis (PBD) and those impacting specific peroxisomal factors. Prior studies have indicated a role for acylcarnitine testing in the diagnosis of some peroxisomal diseases through the detection of long chain dicarboxylic acylcarnitine abnormalities (C16-DC and C18-DC). However, there remains limited independent corroboration of these initial findings and acylcarnitine testing for peroxisomal diseases has not been widely adopted in clinical laboratories. To explore the utility of acylcarnitine testing in the diagnosis of peroxisomal disorders we applied a LC-MS/MS acylcarnitine method to study a heterogenous clinical sample set (n = 598) that included residual plasma specimens from nineteen patients with PBD caused by PEX1 or PEX6 deficiency, ranging in severity from lethal neonatal onset to mild late onset forms. Multiple dicarboxylic acylcarnitines were significantly elevated in PBD patients including medium to long chain (C8-DC to C18-DC) species as well as previously undescribed elevations of malonylcarnitine (C3-DC) and very long chain dicarboxylic acylcarnitines (C20-DC and C22-DC). The best performing plasma acylcarnitine biomarkers, C20-DC and C22-DC, were detected at elevated levels in 100% and 68% of PBD patients but were rarely elevated in patients that did not have a PBD. We extended our analysis to residual newborn screening blood spot cards and were able to detect dicarboxylic acylcarnitine abnormalities in a newborn with a PBD caused by PEX6 deficiency. Similar to prior studies, we failed to detect substantial dicarboxylic acylcarnitine abnormalities in blood spot cards from patients with x-linked adrenoleukodystrophy (x-ald) indicating that these biomarkers may have utility in quickly narrowing the differential diagnosis in patients with a positive newborn screen for x-ald. Overall, our study identifies widespread dicarboxylic acylcarnitine abnormalities in patients with PBD and highlights key acylcarnitine biomarkers for the detection of this class of inherited metabolic disease.
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    Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype-phenotype correlation
    (Springer Nature, 2019-04) Koczkowska, Magdalena; Callens, Tom; Gomes, Alicia; Sharp, Angela; Chen, Yunjia; Hicks, Alesha D.; Aylsworth, Arthur S.; Azizi, Amedeo A.; Basel, Donald G.; Bellus, Gary; Bird, Lynne M.; Blazo, Maria A.; Burke, Leah W.; Cannon, Ashley; Collins, Felicity; DeFilippo, Colette; Denayer, Ellen; Digilio, Maria C.; Dills, Shelley K.; Dosa, Laura; Greenwood, Robert S.; Griffis, Cristin; Gupta, Punita; Hachen, Rachel K.; Hernández-Chico, Concepción; Janssens, Sandra; Jones, Kristi J.; Jordan, Justin T.; Kannu, Peter; Korf, Bruce R.; Lewis, Andrea M.; Listernick, Robert H.; Lonardo, Fortunato; Mahoney, Maurice J.; Ojeda, Mayra Martinez; McDonald, Marie T.; McDougall, Carey; Mendelsohn, Nancy; Miller, David T.; Mori, Mari; Oostenbrink, Rianne; Perreault, Sebastién; Pierpont, Mary Ella; Piscopo, Carmelo; Pond, Dinel A.; Randolph, Linda M.; Rauen, Katherine A.; Rednam, Surya; Rutledge, S. Lane; Saletti, Veronica; Schaefer, G. Bradley; Schorry, Elizabeth K.; Scott, Daryl A.; Shugar, Andrea; Siqveland, Elizabeth; Starr, Lois J.; Syed, Ashraf; Trapane, Pamela L.; Ullrich, Nicole J.; Wakefield, Emily G.; Walsh, Laurence E.; Wangler, Michael F.; Zackai, Elaine; Claes, Kathleen B. M.; Wimmer, Katharina; van Minkelen, Rick; De Luca, Alessandro; Martin, Yolanda; Legius, Eric; Messiaen, Ludwine M.; Neurology, School of Medicine
    PURPOSE: Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. METHODS: A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. RESULTS: None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofibromas. We did not identify any complications, such as symptomatic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_2972del. CONCLUSION: We demonstrate that individuals with the NF1 p.Met992del pathogenic variant have a mild NF1 phenotype lacking clinically suspected plexiform, cutaneous, or subcutaneous neurofibromas. However, learning difficulties are clearly part of the phenotypic presentation in these individuals and will require specialized care.
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    Lessons learned from additional research analyses of unsolved clinical exome cases
    (BioMed Central, 2017-03-21) Eldomery, Mohammad K.; Coban-Akdemir, Zeynep; Harel, Tamar; Rosenfeld, Jill A.; Gambin, Tomasz; Stray-Pedersen, Asbjørg; Küry, Sébastien; Mercier, Sandra; Lessel, Davor; Denecke, Jonas; Wiszniewski, Wojciech; Penney, Samantha; Liu, Pengfei; Bi, Weimin; Lalani, Seema R.; Schaaf, Christian P.; Wangler, Michael F.; Bacino, Carlos A.; Lewis, Richard Alan; Potocki, Lorraine; Graham, Brett H.; Belmont, John W.; Scaglia, Fernando; Orange, Jordan S.; Jhangiani, Shalini N.; Chiang, Theodore; Doddapaneni, Harsha; Hu, Jianhong; Muzny, Donna M.; Xia, Fan; Beaudet, Arthur L.; Boerwinkle, Eric; Eng, Christine M.; Plon, Sharon E.; Sutton, V. Reid; Gibbs, Richard A.; Posey, Jennifer E.; Yang, Yaping; Lupski, James R.; Department of Pathology and Laboratory Medicine, IU School of Medicine
    BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS: Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION: An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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    MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia
    (Wiley, 2021) Meng, Linyan; Isohanni, Pirjo; Shao, Yunru; Graham, Brett H.; Hickey, Scott E.; Brooks, Stephanie; Suomalainen, Anu; Joset, Pascal; Steindl, Katharina; Rauch, Anita; Hackenberg, Annette; High, Frances A.; Armstrong-Javors, Amy; Mencacci, Niccolò E.; Gonzàlez-Latapi, Paulina; Kamel, Walaa A.; Al-Hashel, Jasem Y.; Bustos, Bernabé I.; Hernandez, Alejandro V.; Krainc, Dimitri; Lubbe, Steven J.; Van Esch, Hilde; De Luca, Chiara; Ballon, Katleen; Ravelli, Claudia; Burglen, Lydie; Qebibo, Leila; Calame, Daniel G.; Mitani, Tadahiro; Marafi, Dana; Pehlivan, Davut; Saadi, Nebal W.; Sahin, Yavuz; Maroofian, Reza; Efthymiou, Stephanie; Houlden, Henry; Maqbool, Shazia; Rahman, Fatima; Gu, Shen; Posey, Jennifer E.; Lupski, James R.; Hunter, Jill V.; Wangler, Michael F.; Carroll, Christopher J.; Yang, Yaping; Medical and Molecular Genetics, School of Medicine
    The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum.
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    TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila
    (Elsevier, 2021) Goodman, Lindsey D.; Cope, Heidi; Nil, Zelha; Ravenscroft, Thomas A.; Charng, Wu-Lin; Lu, Shenzhao; Tien, An-Chi; Pfundt, Rolph; Koolen, David A.; Haaxma, Charlotte A.; Veenstra-Knol, Hermine E.; Klein Wassink-Ruiter, Jolien S.; Wevers, Marijke R.; Jones, Melissa; Walsh, Laurence E.; Klee, Victoria H.; Theunis, Miel; Legius, Eric; Steel, Dora; Barwick, Katy E.S.; Kurian, Manju A.; Mohammad, Shekeeb. S.; Dale, Russell C.; Terhal, Paulien A.; van Binsbergen, Ellen; Kirmse, Brian; Robinette, Bethany; Cogné, Benjamin; Isidor, Bertrand; Grebe, Theresa A.; Kulch, Peggy; Hainline, Bryan E.; Sapp, Katherine; Morava, Eva; Klee, Eric W.; Macke, Erica L.; Trapane, Pamela; Spencer, Christopher; Si, Yue; Begtrup, Amber; Moulton, Matthew J.; Dutta, Debdeep; Kanca, Oguz; Undiagnosed Diseases Network; Wangler, Michael F.; Yamamoto, Shinya; Bellen, Hugo J.; Tan, Queenie K.G.; Pediatrics, School of Medicine
    Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities.