Papers by Cornelius Boerkoel
Alzheimer's & Dementia, 2011
combined analyses of cases and controls. Results: In the case+controls analyses, CLU rs11136000 w... more combined analyses of cases and controls. Results: In the case+controls analyses, CLU rs11136000 was significantly associated with better scores for multiple phenotypes from Logical Memory, namely LMDR (b ¼ 0.94, p ¼ 0.0042), LMPR (b ¼ 2.74, p ¼ 0.01) and LMIR (b ¼ 0.69, p ¼ 0.03). Similar results for CLU were obtained in controls-only analyses, where LMDR (b ¼ 0.82, p ¼ 0.0067) and LMPR (b ¼ 1.87, p ¼ 0.015) associations were significant and that for LMIR (b ¼ 0.49, p ¼ 0.07) was marginal. No other significant associations were observed for the combined cases and controls, although marginal associations were noted for PICALM rs3851179 SNP in controls only for LMPR (b ¼ À1.61, p ¼ 0.046) and LMDR (b ¼ À0.54, p ¼ 0.09). Conclusions: Our results show that the CLU rs11136000 SNP, which is associated with reduced risk of AD, is also associated with improved memory scores in non-demented elderly subjects. Thus, in our dataset, the CLU locus had an influence on cognition that was detectable prior to clinical diagnosis of dementia. Though replication is needed, these results provide further support for CLU in AD and suggest a role for cognitive endophenotypes in genetic studies of dementia.
Annals of Clinical and Translational Neurology, 2014
Objective: Early-onset epileptic encephalopathies have been associated with de novo mutations of ... more Objective: Early-onset epileptic encephalopathies have been associated with de novo mutations of numerous ion channel genes. We employed techniques of modern translational medicine to identify a disease-causing mutation, analyze its altered behavior, and screen for therapeutic compounds to treat the proband. Methods: Three modern translational medicine tools were utilized: (1) high-throughput sequencing technology to identify a novel de novo mutation; (2) in vitro expression and electrophysiology assays to confirm the variant protein's dysfunction; and (3) screening of existing drug libraries to identify potential therapeutic compounds. Results: A de novo GRIN2A missense mutation (c.2434C>A; p.L812M) increased the charge transfer mediated by N-methyl-Daspartate receptors (NMDAs) containing the mutant GluN2A-L812M subunit. In vitro analysis with NMDA receptor blockers indicated that GLuN2A-L812Mcontaining NMDARs retained their sensitivity to the use-dependent channel blocker memantine; while screening of a previously reported GRIN2A mutation (N615K) with these compounds produced contrasting results. Consistent with these data, adjunct memantine therapy reduced our proband's seizure burden. Interpretation: This case exemplifies the potential for personalized genomics and therapeutics to be utilized for the early diagnosis and treatment of infantile-onset neurological disease.
Additional file 3: Table S2. O-glycan analysis results of UDP-3331 and UW172-4 primary dermal fib... more Additional file 3: Table S2. O-glycan analysis results of UDP-3331 and UW172-4 primary dermal fibroblasts.
Additional file 2: Figure S1. Overview of N- and O-linked glycosylation pathways. N-linked glycos... more Additional file 2: Figure S1. Overview of N- and O-linked glycosylation pathways. N-linked glycosylation begins with the synthesis of the dolichol phosphate-linked glycan precursor on the cytosolic face of the endoplasmic reticulum (E.R.). Once the precursor molecule is flipped into the E.R. lumen, it is further built up before being transferred to the nascent polypeptide. After the glycosylated polypeptide is properly folded, it is transferred to the cis Golgi where the high-37 mannose species are trimmed and further matured by the addition N-acetylglucosamine (GlcNAc), followed by galactose, fucose and, finally, sialic acid to form the most prevalent, Complex N-linked glycans. An alternative pathway to generate Hybrid glycan structures also exists. The enzymes that perform each of these glycan-building steps are targeted to either cis, medial, or trans Golgi stacks to facilitate proper assembly of the sugars. Two representative O-linked glycosylation pathways are shown: O-GalNAc a...
Additional file 1: Table S1. O-glycan analysis results of UDP-3331 plasma.
Read summary statistics of whole-genome sequencing on Illumina HiSeq 2000 (>Q20). (XLSX 56 kb)
Titration of percentage target exome sequenced as a function of depth of sequencing thresholds. (... more Titration of percentage target exome sequenced as a function of depth of sequencing thresholds. (XLSX 59 kb)
Systematic approach to study exome capture variability in exome-sequencing (A) Three-generation p... more Systematic approach to study exome capture variability in exome-sequencing (A) Three-generation pedigree in which two individuals have an undiagnosed disease that segregated as an autosomal dominant disorder and a de novo variation arose in the second generation. (B) Model of individual subject sample blood DNA processing and sequencing. A sample of blood went through DNA isolation, and independent libraries (in triplicate) were sequenced to appropriate comparable depth and analyzed for various quality control parameters, target coverage, read depth and nucleotide variation detection. (C) Schematic illustration of sequencing read depth vs. targeted genomic region in relation to exome sequencing in replicate. Listed are also the main approaches taken in this study to analyzed exome replicate data. (D) Two main hypotheses tested using replicate exome data: (i) Biases in sequence capture resulting in poor coverage are addressable through repetition (ii) Library replication is beneficia...
Ablepharon macrostomia syndrome (AMS) and Barber-Say syndrome (BSS) are rare congenital ectoderma... more Ablepharon macrostomia syndrome (AMS) and Barber-Say syndrome (BSS) are rare congenital ectodermal dysplasias characterized by similar clinical features. To establish the genetic basis of AMS and BSS, we performed extensive clinical phenotyping, whole exome and candidate gene sequencing, and functional validations. We identified a recurrent de novo mutation in TWIST2 in seven independent AMS-affected families, as well as another recurrent de novo mutation affecting the same amino acid in ten independent BSS-affected families. Moreover, a genotype-phenotype correlation was observed, because the two syndromes differed based solely upon the nature of the substituting amino acid: a lysine at TWIST2 residue 75 resulted in AMS, whereas a glutamine or alanine yielded BSS. TWIST2 encodes a basic helix-loop-helix transcription factor that regulates the development of mesenchymal tissues. All identified mutations fell in the basic domain of TWIST2 and altered the DNA-binding pattern of Flag-TWIST2 in HeLa cells. Comparison of wild-type and mutant TWIST2 expressed in zebrafish identified abnormal developmental phenotypes and widespread transcriptome changes. Our results suggest that autosomal-dominant TWIST2 mutations cause AMS or BSS by inducing protean effects on the transcription factor's DNA binding.
Atlas of X-Linked Intellectual Disability Syndromes, 2011
CLINICAL CHARACTERISTICS: Snyder-Robinson syndrome (SRS) is an X-linked intellectual disability s... more CLINICAL CHARACTERISTICS: Snyder-Robinson syndrome (SRS) is an X-linked intellectual disability syndrome characterized by asthenic build, facial dysmorphism with a prominent lower lip, kyphoscoliosis, osteoporosis, speech abnormalities, and seizures. Developmental delay usually presents as failure to meet early developmental milestones and then evolves to moderate to profound intellectual disability (which appears to remain stable over time) and variable motor disability. Asthenic habitus and low muscle mass usually develop during the first year, even in males who are ambulatory. During the first decade, males with SRS develop osteoporosis, resulting in fractures in the absence of trauma. DIAGNOSIS/TESTING: The diagnosis of SRS is established by identification of a hemizygous loss-of-function SMS pathogenic variant on molecular genetic testing. MANAGEMENT: Treatment of manifestations: Speech, physical, and/or occupational therapy may be helpful. Standard surgical treatment by craniofacial team for those with cleft palate. Calcium supplementation has slightly improved bone mineral density in a few individuals. Standard management of kyphoscoliosis by orthopedics. Seizures have shown varying responses to anti-seizure medications; Carbamazepine, phenobarbital, clobazam, levetiracetam, and valproic acid have been used successfully in some individuals. Surveillance: Monitor developmental progress and educational needs. Clinical examination and DEXA scans to evaluate for progression of osteoporosis and investigate for factures if medically indicated. While receiving calcium supplementation, individuals should be evaluated regularly for ectopic calcification by endocrinology. Clinical examinations for kyphoscoliosis at each visit. Monitor those with seizures as clinically indicated. GENETIC COUNSELING: SRS is inherited in an X-linked manner. If the mother of the proband has a pathogenic variant, the chance of transmitting it in each pregnancy is 50%: Males who inherit the pathogenic variant will be affected; females who inherit the pathogenic variant will be carriers (to date, features of SRS have not been observed in heterozygous females). Affected males are not known to reproduce. Once an SMS pathogenic variant is identified in an affected family member, carrier testing for at-risk relatives, prenatal testing for pregnancies at increased risk, and preimplantation genetic testing are possible.
Supplementary Methods, Tables, and Figures. (PDF 45904 kb)
Molecular Brain Research, 1995
Emerging evidence suggests that lysophosphatidic acid (LPA) is a physiological regulator of cyclo... more Emerging evidence suggests that lysophosphatidic acid (LPA) is a physiological regulator of cyclooxygenase-2 (Cox-2) expression. Herein we used ovarian cancer cells as a model to investigate the molecular mechanisms that link the LPA G proteincoupled receptors (GPCRs) to Cox-2 expression. LPA stimulated Cox-2 expression and release of prostaglandins though the LPA 1 , LPA 2 , and LPA 5 receptors. The effect of LPA involves both transcriptional activation and post-transcriptional enhancement of Cox-2 mRNA stability. The consensus sites for C/EBP in the Cox-2 promoter were essential for transcriptional activation of Cox-2 by LPA. The NF-B and AP-1 transcription factors commonly involved in inducible Cox-2 expression were dispensable. Dominant-negative C/EPB inhibited LPA activation of the Cox-2 promoter and expression. Furthermore, LPA stimulated C/EBP phosphorylation and activity through a novel mechanism integrating GPCR signals and a permissive activity from a receptor tyrosine kinase (RTK). This role of RTK was not consistent with LPA activation of C/EBP through transactivation of RTK, as full activation of RTKs with their own agonists only weakly stimulated C/EBP. In addition to the transcriptional activation, the RNA stabilization protein HuR bound to and protected Cox-2 mRNA in LPA-stimulated cells, indicating an active role for HuR in sustaining Cox-2 induction during physiological responses.
Translational Research
The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) studies rare genetic d... more The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) studies rare genetic disorders not only to achieve diagnoses, but to understand human biology. To ascertain the contribution of protein glycosylation to rare diseases, the NIH UDP used mass spectrometry to agnostically identify abnormalities of N-linked and O-linked glycans in plasma and free oligosaccharides in the urine of 207 patients. 60% of UDP patients had a glycome profile that deviated from control values in at least 1 fluid. Additional evaluation of the fibroblast glycome in 66 patients with abnormalities in plasma and/or urine revealed a consistent glycome phenotype in 83% of these cases. Many of these patients may have secondary glycosylation defects, since it is unlikely that they all have congenital disorders of glycosylation (CDGs). In fact, whole exome sequencing revealed only a few patients with CDGs, along with several others having disorders indirectly altering glycosylation. In summary, we describe a biochemical phenotyping screen to identify defects in protein glycosylation that can elucidate mechanisms of disease among NIH UDP patients.
Scientific reports, Jan 9, 2018
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a nuclear and mitochondrial protein that in nuclei and ... more Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a nuclear and mitochondrial protein that in nuclei and in vitro repairs blocked 3' DNA termini such as 3' phosphotyrosine conjugates resulting from stalling of topoisomerase I-DNA intermediates. Its mutation also causes spinocerebellar ataxia with axonal neuropathy type 1 (SCAN1). Because Tdp1 colocalizes with mitochondria following oxidative stress, we hypothesized that Tdp1 repairs mitochondrial DNA (mtDNA) and that mtDNA damage mediates entry of Tdp1 into the mitochondria. To test this, we used S. cerevisiae mutants, cultured mouse and human cells, and a Tdp1 knockout mouse. HO- and rotenone-induced cellular and intramitochondrial reactive oxygen species (ROS) activated oxidant-responsive kinases P38 and ERK1, and the translocation of Tdp1 from the nucleus to the mitochondria via the TIM/TOM complex. This translocation occurred independently of mtDNA. Within the mitochondria, Tdp1 interacted with Ligase III and reduced mtDNA mutat...
Nature communications, Jan 18, 2018
The originally published version of this Article contained errors in Figure 1. In panel c, the gr... more The originally published version of this Article contained errors in Figure 1. In panel c, the grey shading denoting evolutionary conservation and the arrowheads indicating amino acids affected in Snyder-Robinson syndrome were displaced relative to the sequence. These errors have now been corrected in both the PDF and HTML versions of the manuscript.
Nucleus (Austin, Tex.), 2016
Mutations in SMARCAL1, which encodes a DNA annealing helicase with roles in DNA replication fork ... more Mutations in SMARCAL1, which encodes a DNA annealing helicase with roles in DNA replication fork restart, DNA repair, and gene expression modulation, cause Schimke immuno-osseous dysplasia (SIOD), an autosomal recessive disease characterized by skeletal dysplasia, renal disease, T-cell immunodeficiency, and arteriosclerosis. The clinical features of SIOD arise from pathological changes in gene expression; however, the underlying mechanism for these gene expression alterations remains unclear. We hypothesized that changes of the epigenome alter gene expression in SIOD. To test this, we performed a genetic screen for interaction between Marcal1, the Drosophila melanogaster ortholog of SMARCAL1, and the genes of the trithorax group (trxG) and Polycomb group (PcG), which encode epigenetic regulators. SMARCAL1 and Marcal1 genetically interacted with trxG and PcG members. A homozygous null mutation of Marcal1 suppressed the wing-to-haltere transformation, ectopic Ultrabithorax (Ubx) expre...
Frontiers in medicine, 2017
Traditionally, the use of genomic information for personalized medical decisions relies on prior ... more Traditionally, the use of genomic information for personalized medical decisions relies on prior discovery and validation of genotype-phenotype associations. This approach constrains care for patients presenting with undescribed problems. The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) hypothesized that defining disease as maladaptation to an ecological niche allows delineation of a logical framework to diagnose and evaluate such patients. Herein, we present the philosophical bases, methodologies, and processes implemented by the NIH UDP. The NIH UDP incorporated use of the Human Phenotype Ontology, developed a genomic alignment strategy cognizant of parental genotypes, pursued agnostic biochemical analyses, implemented functional validation, and established virtual villages of global experts. This systematic approach provided a foundation for the diagnostic or non-diagnostic answers provided to patients and serves as a paradigm for scalable translational ...
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Papers by Cornelius Boerkoel