1
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Walters ME, Lacassie Y, Azamian M, Franciskovich R, Zapata G, Hernandez PP, Liu P, Campbell IM, Bostwick BL, Lalani SR. Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1. Am J Med Genet A 2020; 185:916-922. [PMID: 33369125 DOI: 10.1002/ajmg.a.62036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 11/08/2022]
Abstract
ALX4 is a homeobox gene expressed in the mesenchyme of developing bone and is known to play an important role in the regulation of osteogenesis. Enlarged parietal foramina (EPF) is a phenotype of delayed intramembranous ossification of calvarial bones due to variants of ALX4. The contrasting phenotype of premature ossification of sutures is observed with heterozygous loss-of-function variants of TWIST1, which is an important regulator of osteoblast differentiation. Here, we describe an individual with a large cranium defect, with dominant transmission from the mother, both carrying disease causing heterozygous variants in ALX4 and TWIST1. The distinct phenotype of absent superior and posterior calvarium in the child and his mother was in sharp contrast to the other affected maternal relatives with a recognizable ALX4-related EPF phenotype. This report demonstrates comorbid disorders of Saethre-Chotzen syndrome and EPF in a mother and her child, resulting in severe skull defects reminiscent of calvarial abnormalities observed with bilallelic ALX4 variants. To our knowledge this is the first instance of ALX4 and TWIST1 variants acting synergistically to cause a unique phenotype influencing skull ossification.
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Affiliation(s)
- Michelle E Walters
- Division of Dermatology, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Yves Lacassie
- Division of Genetics, Department of Pediatrics, Louisiana State University Health Sciences Center School of Medicine, and Children's Hospital, New Orleans, Louisiana, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Gladys Zapata
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia P Hernandez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Bret L Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
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2
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Burk CM, Coffey KE, Mace EM, Bostwick BL, Chinn IK, Coban-Akdemir ZH, Jhangiani SN, Lupski JR, Ortiz D, Barnum JL, Allen SW, Robertson LM, Orange JS, Chong HJ. Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with NK dysfunction and EBV-driven malignancy treated with stem cell transplantation. J Allergy Clin Immunol Pract 2019; 8:1103-1106.e3. [PMID: 31520839 DOI: 10.1016/j.jaip.2019.08.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Caitlin M Burk
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa.
| | - Kara E Coffey
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Emily M Mace
- Columbia University Irving Medical Center, New York, NY
| | - Bret L Bostwick
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | - Ivan K Chinn
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | | | | | - James R Lupski
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Jessie L Barnum
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Steven W Allen
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Leanna-Marie Robertson
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | | | - Hey J Chong
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
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3
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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4
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LD, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:456. [PMID: 30193138 PMCID: PMC6128320 DOI: 10.1016/j.ajhg.2018.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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5
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Poli MC, Ebstein F, Nicholas SK, de Guzman MM, Forbes LR, Chinn IK, Mace EM, Vogel TP, Carisey AF, Benavides F, Coban-Akdemir ZH, Gibbs RA, Jhangiani SN, Muzny DM, Carvalho CM, Schady DA, Jain M, Rosenfeld JA, Emrick L, Lewis RA, Lee B, Zieba BA, Küry S, Krüger E, Lupski JR, Bostwick BL, Orange JS, Orange JS. Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome. Am J Hum Genet 2018; 102:1126-1142. [PMID: 29805043 DOI: 10.1016/j.ajhg.2018.04.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
The proteasome processes proteins to facilitate immune recognition and host defense. When inherently defective, it can lead to aberrant immunity resulting in a dysregulated response that can cause autoimmunity and/or autoinflammation. Biallelic or digenic loss-of-function variants in some of the proteasome subunits have been described as causing a primary immunodeficiency disease that manifests as a severe dysregulatory syndrome: chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE). Proteasome maturation protein (POMP) is a chaperone for proteasome assembly and is critical for the incorporation of catalytic subunits into the proteasome. Here, we characterize and describe POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity. We also begin to delineate a complex genetic mechanism whereby de novo heterozygous frameshift variants in the penultimate exon of POMP escape nonsense-mediated mRNA decay (NMD) and result in a truncated protein that perturbs proteasome assembly by a dominant-negative mechanism. To our knowledge, this mechanism has not been reported in any primary immunodeficiencies, autoinflammatory syndromes, or autoimmune diseases. Here, we define a unique hypo- and hyper-immune phenotype and report an immune dysregulation syndrome caused by frameshift mutations that escape NMD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jordan S Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Division of Pediatric Immunology, Allergy, and Rheumatology, Houston, TX 77030, USA.
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6
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Petersen AK, Streff H, Tokita M, Bostwick BL. The first reported case of an inherited pathogenic
CHD2
variant in a clinically affected mother and daughter. Am J Med Genet A 2018; 176:1667-1669. [DOI: 10.1002/ajmg.a.38835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 04/04/2018] [Accepted: 04/15/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Andrea Klunder Petersen
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
- Department of PediatricsBaylor College of MedicineHouston Texas
- Randall Children's HospitalPortland Oregon
| | - Haley Streff
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
- Texas Children's HospitalHouston Texas
| | - Mari Tokita
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
| | - Bret L. Bostwick
- Department of Molecular and Human GeneticsBaylor College of MedicineHouston Texas
- Texas Children's HospitalHouston Texas
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7
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Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, Zhang J, He W, Dharmadhikari AV, Qu C, Ward P, Braxton A, Narayanan S, Ge X, Tokita MJ, Santiago-Sim T, Dai H, Chiang T, Smith H, Azamian MS, Robak L, Bostwick BL, Schaaf CP, Potocki L, Scaglia F, Bacino CA, Hanchard NA, Wangler MF, Scott D, Brown C, Hu J, Belmont JW, Burrage LC, Graham BH, Sutton VR, Craigen WJ, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Muzny DM, Miller MJ, Wang X, Leduc MS, Xiao R, Liu P, Shaw C, Walkiewicz M, Bi W, Xia F, Lee B, Eng C, Yang Y, Lalani SR. Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. JAMA Pediatr 2017; 171:e173438. [PMID: 28973083 PMCID: PMC6359927 DOI: 10.1001/jamapediatrics.2017.3438] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance While congenital malformations and genetic diseases are a leading cause of early infant death, to our knowledge, the contribution of single-gene disorders in this group is undetermined. Objective To determine the diagnostic yield and use of clinical exome sequencing in critically ill infants. Design, Setting, and Participants Clinical exome sequencing was performed for 278 unrelated infants within the first 100 days of life who were admitted to Texas Children's Hospital in Houston, Texas, during a 5-year period between December 2011 and January 2017. Exome sequencing types included proband exome, trio exome, and critical trio exome, a rapid genomic assay for seriously ill infants. Main Outcomes and Measures Indications for testing, diagnostic yield of clinical exome sequencing, turnaround time, molecular findings, patient age at diagnosis, and effect on medical management among a group of critically ill infants who were suspected to have genetic disorders. Results The mean (SEM) age for infants participating in the study was 28.5 (1.7) days; of these, the mean (SEM) age was 29.0 (2.2) days for infants undergoing proband exome sequencing, 31.5 (3.9) days for trio exome, and 22.7 (3.9) days for critical trio exome. Clinical indications for exome sequencing included a range of medical concerns. Overall, a molecular diagnosis was achieved in 102 infants (36.7%) by clinical exome sequencing, with relatively low yield for cardiovascular abnormalities. The diagnosis affected medical management for 53 infants (52.0%) and had a substantial effect on informed redirection of care, initiation of new subspecialist care, medication/dietary modifications, and furthering life-saving procedures in select patients. Critical trio exome sequencing revealed a molecular diagnosis in 32 of 63 infants (50.8%) at a mean (SEM) of 33.1 (5.6) days of life with a mean (SEM) turnaround time of 13.0 (0.4) days. Clinical care was altered by the diagnosis in 23 of 32 patients (71.9%). The diagnostic yield, patient age at diagnosis, and medical effect in the group that underwent critical trio exome sequencing were significantly different compared with the group who underwent regular exome testing. For deceased infants (n = 81), genetic disorders were molecularly diagnosed in 39 (48.1%) by exome sequencing, with implications for recurrence risk counseling. Conclusions and Relevance Exome sequencing is a powerful tool for the diagnostic evaluation of critically ill infants with suspected monogenic disorders in the neonatal and pediatric intensive care units and its use has a notable effect on clinical decision making.
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Affiliation(s)
- Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Mohan Pammi
- Department of Pediatrics, Section of Neonatology, Baylor College of Medicine, Houston, Texas
| | - Anirudh Saronwala
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrew Ray Ghazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Jing Zhang
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin He
- Baylor Genetics Laboratory, Houston, Texas
| | | | | | - Patricia Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Swetha Narayanan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mari J. Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Theodore Chiang
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Hadley Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret L. Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, Texas
| | - Daryl Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston Texas
| | - Chester Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center
| | - Jianhong Hu
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Vernon Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - William J. Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Donna M. Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston Texas
| | - Marcus J. Miller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Magalie S. Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics Laboratory, Houston, Texas
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8
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Bostwick BL, McLean S, Posey JE, Streff HE, Gripp KW, Blesson A, Powell-Hamilton N, Tusi J, Stevenson DA, Farrelly E, Hudgins L, Yang Y, Xia F, Wang X, Liu P, Walkiewicz M, McGuire M, Grange DK, Andrews MV, Hummel M, Madan-Khetarpal S, Infante E, Coban-Akdemir Z, Miszalski-Jamka K, Jefferies JL, Rosenfeld JA, Emrick L, Nugent KM, Lupski JR, Belmont JW, Lee B, Lalani SR. Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Genome Med 2017; 9:73. [PMID: 28807008 PMCID: PMC5557075 DOI: 10.1186/s13073-017-0463-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Background De novo missense variants in CDK13 have been described as the cause of syndromic congenital heart defects in seven individuals ascertained from a large congenital cardiovascular malformations cohort. We aimed to further define the phenotypic and molecular spectrum of this newly described disorder. Methods To minimise ascertainment bias, we recruited nine additional individuals with CDK13 pathogenic variants from clinical and research exome laboratory sequencing cohorts. Each individual underwent dysmorphology exam and comprehensive medical history review. Results We demonstrate greater than expected phenotypic heterogeneity, including 33% (3/9) of individuals without structural heart disease on echocardiogram. There was a high penetrance for a unique constellation of facial dysmorphism and global developmental delay, as well as less frequently seen renal and sacral anomalies. Two individuals had novel CDK13 variants (p.Asn842Asp, p.Lys734Glu), while the remaining seven unrelated individuals had a recurrent, previously published p.Asn842Ser variant. Summary of all variants published to date demonstrates apparent restriction of pathogenic variants to the protein kinase domain with clustering in the ATP and magnesium binding sites. Conclusions Here we provide detailed phenotypic and molecular characterisation of individuals with pathogenic variants in CDK13 and propose management guidelines based upon the estimated prevalence of anomalies identified. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0463-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bret L Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Haley E Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Alyssa Blesson
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Nina Powell-Hamilton
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - Jessica Tusi
- Division of Medical Genetics, A.I. duPont Hospital for Children/Nemours, Wilmington, DE, USA
| | - David A Stevenson
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ellyn Farrelly
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Baylor Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marisa V Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marybeth Hummel
- Department of Pediatrics, Section of Medical Genetics, West Virginia University Health Sciences Center, Morgantown, WV, USA
| | | | - Elena Infante
- Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Karol Miszalski-Jamka
- Division of Magnetic Resonance Imaging, Silesian Center for Heart Disease, Zabrze, Poland
| | - John L Jefferies
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, 6701 Fannin St, Suite 1560, Houston, TX, 77030, USA
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Zuleger CL, Macklin MD, Bostwick BL, Pei Q, Newton MA, Albertini MR. In vivo 6-thioguanine-resistant T cells from melanoma patients have public TCR and share TCR beta amino acid sequences with melanoma-reactive T cells. J Immunol Methods 2010; 365:76-86. [PMID: 21182840 DOI: 10.1016/j.jim.2010.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 12/01/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
In vivo hypoxanthine-guanine phosphoribosyltransferase (HPRT)-deficient T cells (MT) from melanoma patients are enriched for T cells with in vivo clonal amplifications that traffic between blood and tumor tissues. Melanoma is thus a model cancer to test the hypothesis that in vivo MT from cancer patients can be used as immunological probes for immunogenic tumor antigens. MT were obtained by 6-thioguanine (TG) selection of lymphocytes from peripheral blood and tumor tissues, and wild-type T cells (WT) were obtained analogously without TG selection. cDNA sequences of the T cell receptor beta chains (TRB) were used as unambiguous biomarkers of in vivo clonality and as indicators of T cell specificity. Public TRB were identified in MT from the blood and tumor of different melanoma patients. Such public TRB were not found in normal control MT or WT. As an indicator of T cell specificity for melanoma, the >2600 MT and WT TRB, including the public TRB from melanoma patients, were compared to a literature-derived empirical database of >1270 TRB from melanoma-reactive T cells. Various degrees of similarity, ranging from 100% conservation to 3-amino acid motifs (3-mer), were found between both melanoma patient MT and WT TRBs and the empirical database. The frequency of 3-mer and 4-mer TRB matching to the empirical database was significantly higher in MT compared with WT in the tumor (p=0.0285 and p=0.006, respectively). In summary, in vivo MT from melanoma patients contain public TRB as well as T cells with specificity for characterized melanoma antigens. We conclude that in vivo MT merit study as novel probes for uncharacterized immunogenic antigens in melanoma and other malignancies.
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