Publications by authors named "Alyssa Tran"

12 Publications

  • Page 1 of 1

COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay.

Am J Hum Genet 2021 09 26;108(9):1710-1724. Epub 2021 Aug 26.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

Coatomer complexes function in the sorting and trafficking of proteins between subcellular organelles. Pathogenic variants in coatomer subunits or associated factors have been reported in multi-systemic disorders, i.e., coatopathies, that can affect the skeletal and central nervous systems. We have identified loss-of-function variants in COPB2, a component of the coatomer complex I (COPI), in individuals presenting with osteoporosis, fractures, and developmental delay of variable severity. Electron microscopy of COPB2-deficient subjects' fibroblasts showed dilated endoplasmic reticulum (ER) with granular material, prominent rough ER, and vacuoles, consistent with an intracellular trafficking defect. We studied the effect of COPB2 deficiency on collagen trafficking because of the critical role of collagen secretion in bone biology. COPB2 siRNA-treated fibroblasts showed delayed collagen secretion with retention of type I collagen in the ER and Golgi and altered distribution of Golgi markers. copb2-null zebrafish embryos showed retention of type II collagen, disorganization of the ER and Golgi, and early larval lethality. Copb2 mice exhibited low bone mass, and consistent with the findings in human cells and zebrafish, studies in Copb2 mouse fibroblasts suggest ER stress and a Golgi defect. Interestingly, ascorbic acid treatment partially rescued the zebrafish developmental phenotype and the cellular phenotype in Copb2 mouse fibroblasts. This work identifies a form of coatopathy due to COPB2 haploinsufficiency, explores a potential therapeutic approach for this disorder, and highlights the role of the COPI complex as a regulator of skeletal homeostasis.
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http://dx.doi.org/10.1016/j.ajhg.2021.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8456174PMC
September 2021

De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation.

Am J Hum Genet 2020 04 19;106(4):570-583. Epub 2020 Mar 19.

Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA.

EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
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http://dx.doi.org/10.1016/j.ajhg.2020.02.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118694PMC
April 2020

Recurrent mosaic MTOR c.5930C > T (p.Thr1977Ile) variant causing megalencephaly, asymmetric polymicrogyria, and cutaneous pigmentary mosaicism: Case report and review of the literature.

Am J Med Genet A 2019 03 19;179(3):475-479. Epub 2018 Dec 19.

Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas.

Genetic alterations leading to overactivation of mammalian target of rapamycin (mTOR) signaling result in brain overgrowth syndromes such as focal cortical dysplasia (FCD) and megalencephaly. Megalencephaly with cutis tri-color of the Blaschko-linear type pigmentary mosaicism and intellectual disability is a rare neurodevelopmental disorder attributed to the recurrent mosaic c.5930C > T (p.Thr1977Ile) MTOR variant. This variant was previously reported at low to intermediate levels of mosaicism in the peripheral blood of three unrelated individuals with consistent clinical findings. We report a fourth case of a 3-year-old female presenting with megalencephaly, obstructive hydrocephalus due to cerebral aqueductal stenosis, asymmetric polymicrogyria, dysgenesis of the corpus callosum, hypotonia, developmental delay, and cutaneous pigmentary mosaicism. Oligonucleotide and SNP chromosomal microarray (CMA), karyotype, and trio whole exome sequencing (WES) in the peripheral blood, as well as a targeted gene variant panel from fibroblasts derived from hyperpigmented and non-hyperpigmented skin did not detect any abnormalities in MTOR or other genes associated with brain overgrowth syndromes. Unlike the previously reported cases, the de novo c.5930C > T (p.Thr1977Ile) MTOR variant was detected at 32% mosaicism in our patient only after WES was performed on fibroblast-derived DNA from the hyperpigmented skin. This case demonstrates the tissue variability in mosaic expression of the recurrent p.Thr1977Ile MTOR variant, emphasizes the need for skin biopsies in the genetic evaluation of patients with skin pigmentary mosaicism, and expands the clinical phenotype associated with this pathogenic MTOR variant.
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http://dx.doi.org/10.1002/ajmg.a.61007DOI Listing
March 2019

Whole-Exome Sequencing Identifies an Intronic Cryptic Splice Site in Causing Osteogenesis Imperfecta Type VI.

JBMR Plus 2018 Jul 16;2(4):235-239. Epub 2018 Apr 16.

Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA.

The heritable disorder osteogenesis imperfecta (OI) is characterized by bone fragility and low bone mass. OI type VI is an autosomal recessive form of the disorder with moderate to severe bone fragility. OI type VI is caused by mutations in the serpin peptidase inhibitor, clade F, member 1 (), the gene coding for pigment epithelium-derived factor (PEDF). Here, we report a patient with OI type VI caused by a novel homozygous intronic variant in identified by whole-exome sequencing (WES). The mutation was not identified using a low bone mass gene panel based on next-generation sequencing. This variant creates a novel consensus splice donor site (AGGC to AGGT) in intron 4. Analysis of cDNA generated from fibroblasts revealed retention of a 32-bp intronic fragment between exons 4 and 5 in the cDNA, a result of alternative splicing from the novel splice-donor site. As a result, the aberrant insertion of this intronic fragment generated a frameshift pathogenic variant and induced nonsense-mediated decay. Furthermore, gene expression by quantitative PCR showed expression was dramatically reduced in patient fibroblasts, and PEDF level was also significantly reduced in the patient's plasma. In conclusion, we report a novel homozygous variant that generates an alternative splice-donor in intron 4 of which gives rise to severe bone fragility. The work also demonstrates clinical utility of WES analysis, and consideration of noncoding variants, in the diagnostic setting of rare bone diseases. © 2018 The Authors. is published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
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http://dx.doi.org/10.1002/jbm4.10044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124173PMC
July 2018

Neonatal fractures as a presenting feature of LMOD3-associated congenital myopathy.

Am J Med Genet A 2017 Oct 16;173(10):2789-2794. Epub 2017 Aug 16.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Nemaline myopathy is a rare inherited disorder characterized by weakness, hypotonia, and depressed deep tendon reflexes. It is clinically and genetically heterogeneous, with the most severe phenotype presenting as perinatal akinesia, severe muscle weakness, feeding difficulties and respiratory failure, leading to early mortality. Pathogenic variants in 12 genes, encoding components of the sarcomere or factors related to myogenesis, have been reported in patients affected with the disorder. Here, we describe an early, lethal presentation of decreased fetal movements, hypotonia, muscle weakness, and neonatal respiratory failure requiring ventilator support in three siblings from a consanguineous family. All exhibited perinatal fractures, and thus, a skeletal dysplasia was considered as possibly contributing to the phenotype. However, whole exome sequencing revealed a homozygous, loss-of-function pathogenic variant in LMOD3, which has recently been associated with nemaline myopathy and, in a subset of patients, perinatal fractures. This case demonstrates the importance of considering congenital neuromuscular disorders in the differential diagnosis of perinatal fractures.
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http://dx.doi.org/10.1002/ajmg.a.38383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603416PMC
October 2017

Heterozygous variants in ACTL6A, encoding a component of the BAF complex, are associated with intellectual disability.

Hum Mutat 2017 10 10;38(10):1365-1371. Epub 2017 Jul 10.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Pathogenic variants in genes encoding components of the BRG1-associated factor (BAF) chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1. A third subject has a splicing variant that creates an in-frame deletion. Our findings suggest that the variants identified in our subjects may have a deleterious effect on the function of the protein by disturbing the integrity of the BAF complex. Thus, ACTL6A gene mutation analysis should be considered in patients with intellectual disability, learning disabilities, or developmental language disorder.
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http://dx.doi.org/10.1002/humu.23282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599325PMC
October 2017

Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies.

Am J Med Genet A 2017 Mar 26;173(3):733-739. Epub 2016 Nov 26.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.

Spondylometaphyseal dysplasia (SMD) corner fracture type (also known as SMD "Sutcliffe" type, MIM 184255) is a rare skeletal dysplasia that presents with mild to moderate short stature, developmental coxa vara, mild platyspondyly, corner fracture-like lesions, and metaphyseal abnormalities with sparing of the epiphyses. The molecular basis for this disorder has yet to be clarified. We describe two patients with SMD corner fracture type and heterozygous pathogenic variants in COL2A1. These two cases together with a third case of SMD corner fracture type with a heterozygous COL2A1 pathogenic variant previously described suggest that this disorder overlaps with type II collagenopathies. The finding of one of the pathogenic variants in a previously reported case of spondyloepimetaphyseal dysplasia (SEMD) Strudwick type and the significant clinical similarity suggest an overlap between SMD corner fracture and SEMD Strudwick types. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajmg.a.38059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315610PMC
March 2017

Mapping multisensory parietal face and body areas in humans.

Proc Natl Acad Sci U S A 2012 Oct 15;109(44):18114-9. Epub 2012 Oct 15.

Institute for Neural Computation, Department of Electrical and Computer Engineering, and Department of Cognitive Science, University of California at San Diego, La Jolla, CA 92093, USA.

Detection and avoidance of impending obstacles is crucial to preventing head and body injuries in daily life. To safely avoid obstacles, locations of objects approaching the body surface are usually detected via the visual system and then used by the motor system to guide defensive movements. Mediating between visual input and motor output, the posterior parietal cortex plays an important role in integrating multisensory information in peripersonal space. We used functional MRI to map parietal areas that see and feel multisensory stimuli near or on the face and body. Tactile experiments using full-body air-puff stimulation suits revealed somatotopic areas of the face and multiple body parts forming a higher-level homunculus in the superior posterior parietal cortex. Visual experiments using wide-field looming stimuli revealed retinotopic maps that overlap with the parietal face and body areas in the postcentral sulcus at the most anterior border of the dorsal visual pathway. Starting at the parietal face area and moving medially and posteriorly into the lower-body areas, the median of visual polar-angle representations in these somatotopic areas gradually shifts from near the horizontal meridian into the lower visual field. These results suggest the parietal face and body areas fuse multisensory information in peripersonal space to guard an individual from head to toe.
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http://dx.doi.org/10.1073/pnas.1207946109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497759PMC
October 2012

Assessment of bone mineral status in children with Marfan syndrome.

Am J Med Genet A 2012 Sep 7;158A(9):2221-4. Epub 2012 Aug 7.

Department of Pediatric Diabetes and Endocrinology, Baylor College of Medicine, Houston, Texas 77030-3411, USA.

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder with skeletal involvement. It is caused by mutations in fibrillin1 (FBN1) gene resulting in activation of TGF-β, which developmentally regulates bone mass and matrix properties. There is no consensus regarding bone mineralization in children with MFS. Using dual-energy X-ray absorptiometry (DXA), we evaluated bone mineralization in 20 children with MFS unselected for bone problems. z-Scores were calculated based on age, gender, height, and ethnicity matched controls. Mean whole body bone mineral content (BMC) z-score was 0.26±1.42 (P=0.41). Mean bone mineral density (BMD) z-score for whole body was -0.34±1.4 (P=0.29) and lumbar spine was reduced at -0.55±1.34 (P=0.017). On further adjusting for stature, which is usually higher in MFS, mean BMC z-score was reduced at -0.677±1.37 (P=0.04), mean BMD z-score for whole body was -0.82±1.55 (P=0.002) and for lumbar spine was -0.83±1.32 (P=0.001). An increased risk of osteoporosis in MFS is controversial. DXA has limitations in large skeletons because it tends to overestimate BMD and BMC. By adjusting results for height, age, gender, and ethnicity, we found that MFS patients have significantly lower BMC and BMD in whole body and lumbar spine. Evaluation of diet, exercise, vitamin D status, and bone turnover markers will help gain insight into pathogenesis of the reduced bone mass. Further, larger longitudinal studies are required to evaluate the natural history, incidence of fractures, and effects of pharmacological therapy.
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http://dx.doi.org/10.1002/ajmg.a.35540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429634PMC
September 2012

Decreased bone mineralization in children with Noonan syndrome: another consequence of dysregulated RAS MAPKinase pathway?

Mol Genet Metab 2012 Jun 11;106(2):237-40. Epub 2012 Apr 11.

Department of Pediatrics (Division of Endocrinology and Metabolism), Baylor College of Medicine, Houston, TX, USA.

Introduction: Noonan syndrome (NS) is a disorder of RAS- mitogen activated protein kinase (MAPK) pathway with clinical features of skeletal dysplasia. This pathway is essential for regulation of cell differentiation and growth including bone homeostasis. Currently, limited information exists regarding bone mineralization in NS.

Materials And Methods: Using dual-energy X-ray absorptiometry (DXA), bone mineralization was evaluated in 12 subjects (mean age 8.7 years) with clinical features of NS. All subjects underwent genetic testing which showed mutations in PTPN11 gene (N=8) and SOS1 gene (N=1). In a subgroup of subjects with low bone mass, indices of calcium-phosphate metabolism and bone turnover were obtained.

Results: 50% of subjects had low bone mass as measured by DXA. Z-scores for bone mineral content (BMC) were calculated based on age, gender, height, and ethnicity. Mean BMC z-score was marginally decreased at -0.89 {95% CI -2.01 to 0.23; p=0.1}. Mean total body bone mineral density (BMD) z-score was significantly reduced at -1.87 {95% CI -2.73 to -1.0; p=0.001}. Mean height percentile was close to - 2 SD for this cohort, thus total body BMD z-scores were recalculated, adjusting for height age. Adjusted mean total body BMD z-score was less reduced but still significant at -0.82 {95% CI -1.39 to -0.25; p=0.009}. Biochemical evaluation for bone turnover was unremarkable except serum IGF-I and IGF-BP3 levels which were low-normal for age.

Discussion: Children with NS have a significantly lower total body BMD compared to age, gender, ethnicity and height matched controls. In addition, total BMC appears to trend lower in children with NS compared to controls. We conclude that the metabolic bone disease present resulted from a subtle variation in the interplay of osteoclast and osteoblast activity, without clear abnormalities being defined in the metabolism of either. Clinical significance of this finding needs to be validated by larger longitudinal studies. Also, histomorphometric analysis of bone tissue from NS patients and mouse model of NS may further elucidate the relationship between the RAS-MAPK pathway and skeletal homeostasis.
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http://dx.doi.org/10.1016/j.ymgme.2012.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356458PMC
June 2012

Generalized metabolic bone disease in Neurofibromatosis type I.

Mol Genet Metab 2008 May 4;94(1):105-11. Epub 2008 Mar 4.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 635E, Houston, TX 77030, USA.

Skeletal abnormalities are a recognized component of Neurofibromatosis type I (NF1) but a generalized metabolic bone defect in NF1 has not been fully characterized thus far. The purpose of this study was to characterize at the densitometric, biochemical and pathological level the bone involvement in NF1 patients. Using dual energy X-ray absorptiometry (DXA) we analyzed bone status in 73 unselected NF1 subjects, 26 males and 47 females, mainly children and adolescents (mean age: 16.6 years). In a subgroup of subjects with low bone mass, we measured indices of calcium-phosphate metabolism, bone turnover, and bone density before and after vitamin D and calcium treatment. We found statistically significant and generalized reduction in bone mass with the mean lumbar bone mineral density (BMD) z-score being -1.38+/-1.05 (CI 95% -1.62 to -1.13), and whole body bone mineral content (BMC) z-score -0.61+/-1.19 (CI 95% -0.94 to -0.29), both significantly reduced compared to normal controls (p<.001). PTH was moderately elevated and after 4 months of supplemental therapy with calcium and vitamin D, it decreased to the normal range. However, BMD z-scores did not significantly improve after 2 years of follow-up. Histological analysis of bone samples from NF1 patients revealed substantial alteration of bone microarchitecture due mainly to reduced trabecular bone. Our observations are consistent with a generalized bone metabolic defect due to loss of the function of neurofibromin. Early identification of patients with osteoporosis may permit more timely and aggressive treatments to prevent the likely substantial morbidity associated with increased fracture risk later in life.
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http://dx.doi.org/10.1016/j.ymgme.2007.12.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430595PMC
May 2008

RMRP mutations in cartilage-hair hypoplasia.

Am J Med Genet A 2006 Oct;140(19):2121-30

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

Cartilage hair hypoplasia (CHH) or McKusick type metaphyseal chondrodysplasia (MCD) (OMIM # 250250) is due to either the homozygous or compound heterozygous mutations in the nuclear encoded, non-coding RNA gene RMRP. Twenty-seven CHH patients were referred for molecular evaluation of the clinical diagnosis. RMRP mutations were found in 22 patients. The phenotype in one of the five mutation-negative patients was fully congruent with the adopted case definition of CHH. In a second of these patients, the diagnosis of Schmid type MCD (OMIM # 156500) was made and confirmed by the detection of a mutation in the COL10A1 gene. The remaining patients most likely represent one or more MCDs hitherto not yet delineated. The pattern of cumulative growth in infancy and early childhood in the latter four patients was the single feature with greatest negative predictive power for CHH. Fourteen mutations detected here, had not been reported previously. In this ethnically heterogeneous population, we performed a retrospective study to compare the prevalence of clinical features compared to previous reports based mostly on more ethnically homogenous groups.
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http://dx.doi.org/10.1002/ajmg.a.31331DOI Listing
October 2006
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