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Article ; Online: Are CUL3 variants an underreported cause of congenital heart disease?

Di Francesco, Daniela / Swenerton, Anne / Li, Wenhui Laura / Dunham, Christopher / Hendson, Glenda / Boerkoel, Cornelius F

American journal of medical genetics. Part A

2023 Volume 191, Issue 12, Page(s) 2903–2907

Abstract: Complex heart defects (CHD) are a common malformation associated with disruption of developmental pathways. The Cullin-RING ligases (CRLs) are multi-subunit E3 ubiquitin ligases in which Cullin 3 (CUL3) serves as a scaffolding subunit. Heterozygous CUL3 ... ...

Abstract	Complex heart defects (CHD) are a common malformation associated with disruption of developmental pathways. The Cullin-RING ligases (CRLs) are multi-subunit E3 ubiquitin ligases in which Cullin 3 (CUL3) serves as a scaffolding subunit. Heterozygous CUL3 variants have been associated with neurodevelopmental disorders and pseudohypoaldosteronism type IIE. We report a fetus with CHD and a de novo CUL3 variant (NM_003590.4:c.[1549_1552del];[=], p.(Ser517Profs*23)) and review CUL3 variants reported with CHD. We postulate that CUL3 variants predispose to CHD and hypothesize mechanisms of pathogenesis.
MeSH term(s)	Humans ; Cullin Proteins/genetics ; Cullin Proteins/metabolism ; Ubiquitin-Protein Ligases ; Heart Defects, Congenital/genetics
Chemical Substances	Cullin Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; CUL3 protein, human
Language	English
Publishing date	2023-09-04
Publishing country	United States
Document type	Case Reports
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63387
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Article ; Online: Mesenteric cysts, lymphatic leak, and cerebral cavernous malformation in a proband with KRIT1-related disease.

Moller-Hansen, Ashley / Huynh, Stephanie / Boerkoel, Cornelius F / Chin, Hui-Lin

American journal of medical genetics. Part A

2021 Volume 188, Issue 1, Page(s) 332–335

Abstract: Cerebral cavernous malformations (CCMs) of the central nervous system arise sporadically or secondary to genomic variation. Established genetic etiologies include deleterious variants in KRIT1 (CCM1), malcavernin (CCM2), and PDCD10 (CCM3). KRIT1-related ... ...

Abstract	Cerebral cavernous malformations (CCMs) of the central nervous system arise sporadically or secondary to genomic variation. Established genetic etiologies include deleterious variants in KRIT1 (CCM1), malcavernin (CCM2), and PDCD10 (CCM3). KRIT1-related disease has not been described in conjunction with lymphatic defects, although lymphatic defects with abnormal endothelial cell junctions have been observed in mice deficient in HEG1-KRIT1 signaling. We report a proband with CCMs, multiple chylous mesenteric cysts, and chylous ascites with leaky lymphatic vasculature. Clinical short-read exome sequencing detected a disease-associated KRIT1 variant (NM_194456.1:c.[1927C>T];[=], p.(Gln643*)). We postulate an expansion of KRIT1-related disease to include lymphatic malformations and lymphatic endothelial dysfunction.
MeSH term(s)	Animals ; Hemangioma, Cavernous, Central Nervous System/genetics ; Humans ; KRIT1 Protein/genetics ; Lymphocele ; Mesenteric Cyst ; Mice ; Microtubule-Associated Proteins/genetics ; Proto-Oncogene Proteins/genetics ; Signal Transduction
Chemical Substances	KRIT1 Protein ; KRIT1 protein, human ; Krit1 protein, mouse ; Microtubule-Associated Proteins ; Proto-Oncogene Proteins
Language	English
Publishing date	2021-09-24
Publishing country	United States
Document type	Case Reports
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.62510
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Article: Mitofusin 2 Variant Presenting With a Phenotype of Multiple System Atrophy of Cerebellar Subtype.

Elbert, Adrienne / Dixon, Katherine / Shen, Yaoqing / Hamilton, Sara / Boerkoel, Cornelius F / Jones, Steven J / Kanungo, Anish K

Neurology. Genetics

2023 Volume 10, Issue 1, Page(s) e200114

Abstract: Objectives: To investigate the etiology of cerebellar ataxia in an adult male patient.: Methods: We performed standard neurologic assessment and genome sequencing of a 62-year-old man with rapidly progressive balance and gait abnormalities.: ... ...

Abstract	Objectives: To investigate the etiology of cerebellar ataxia in an adult male patient. Methods: We performed standard neurologic assessment and genome sequencing of a 62-year-old man with rapidly progressive balance and gait abnormalities. Results: The propositus exhibited cognitive dysfunction, mild appendicular bradykinesia, prominent appendicular ataxia, dysarthria, and hypomimia with minimal dysautonomic symptoms. Nerve conduction studies showed mild peripheral sensory neuropathy and normal motor nerve conduction velocities. Brain imaging showed progressive cerebellar atrophy and gliosis of the olivopontocerebellar fibers, characterized by T2 hyperintensity within the pons. Genetic testing revealed a likely pathogenic germline variant in Discussion: We describe progressive cerebellar ataxia in an individual with a deleterious variant in
Language	English
Publishing date	2023-12-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2818607-2
ISSN	2376-7839
ISSN	2376-7839
DOI	10.1212/NXG.0000000000200114
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Article ; Online: NOTCH1 loss of the TAD and PEST domain: An antimorph?

Boerkoel, Pierre / Huynh, Stephanie / Yang, Gui Xiang / Boerkoel, Cornelius F / Patel, Millan S / Lehman, Anna / Terry, Jefferson / Elbert, Adrienne

American journal of medical genetics. Part A

2023 Volume 191, Issue 6, Page(s) 1593–1598

Abstract: The Notch proteins play key roles in cell fate determination during development. Germline pathogenic variants in NOTCH1 predispose to a spectrum of cardiovascular malformations including Adams-Oliver syndrome and a wide variety of isolated complex and ... ...

Abstract	The Notch proteins play key roles in cell fate determination during development. Germline pathogenic variants in NOTCH1 predispose to a spectrum of cardiovascular malformations including Adams-Oliver syndrome and a wide variety of isolated complex and simple congenital heart defects. The intracellular C-terminus of the single-pass transmembrane receptor encoded by NOTCH1 contains a transcriptional activating domain (TAD) required for target gene activation and a PEST domain (a sequence rich in proline, glutamic acid, serine, and threonine), regulating protein stability and turnover. We present a patient with a novel variant encoding a truncated NOTCH1 protein without the TAD and PEST domain (NM_017617.4: c.[6626_6629del];[=], p.(Tyr2209CysfsTer38)) and extensive cardiovascular abnormalities consistent with a NOTCH1-mediated mechanism. This variant fails to promote transcription of target genes as assessed by luciferase reporter assay. Given the roles of the TAD and PEST domains in NOTCH1 function and regulation, we hypothesize that loss of both the TAD and the PEST domain results in a stable, loss-of-function protein that acts as an antimorph through competition with wild-type NOTCH1.
MeSH term(s)	Humans ; Receptor, Notch1/genetics ; Ectodermal Dysplasia/genetics ; Scalp Dermatoses/congenital ; Limb Deformities, Congenital/genetics
Chemical Substances	Receptor, Notch1 ; NOTCH1 protein, human
Language	English
Publishing date	2023-03-03
Publishing country	United States
Document type	Case Reports
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63167
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Article ; Online: Naturally occurring splice variants dissect the functional domains of BHC80 and emphasize the need for RNA analysis.

Hejla, Duha / Huynh, Stephanie / Samra, Simran / Richmond, Phillip A / Dalmann, Joshua / Del Bel, Kate L / Byres, Loryn / Lehman, Anna / Turvey, Stuart E / Boerkoel, Cornelius F

American journal of medical genetics. Part A

2024 Volume 194, Issue 6, Page(s) e63548

Abstract: Pathogenic PHF21A variation causes PHF21A-related neurodevelopmental disorders (NDDs). Although amorphic alleles, including haploinsufficiency, have been established as a disease mechanism, increasing evidence suggests that missense variants as well as ... ...

Abstract	Pathogenic PHF21A variation causes PHF21A-related neurodevelopmental disorders (NDDs). Although amorphic alleles, including haploinsufficiency, have been established as a disease mechanism, increasing evidence suggests that missense variants as well as frameshift variants extending the BHC80 carboxyl terminus also cause disease. Expanding on these, we report a proposita with intellectual disability and overgrowth and a novel de novo heterozygous PHF21A splice variant (NM_001352027.3:c.[153+1G>C];[=]) causing skipping of exon 6, which encodes an in-frame BHC80 deletion (p.(Asn30_Gln51del)). This deletion disrupts a predicted leucine zipper domain and implicates this domain in BHC80 function and as a target of variation causing PHF21A-related NDDs. This extension of understanding emphasizes the application of RNA analysis in precision genomic medicine practice.
MeSH term(s)	Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; RNA Splicing/genetics ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/pathology ; Male ; Exons/genetics ; Female ; Alleles ; Sequence Analysis, RNA
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63548
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Article ; Online: Pan-cancer RNA-seq data stratifies tumours by some hallmarks of cancer.

Frost, F Graeme / Cherukuri, Praveen F / Milanovich, Samuel / Boerkoel, Cornelius F

Journal of cellular and molecular medicine

2019 Volume 24, Issue 1, Page(s) 418–430

Abstract: Numerous genetic and epigenetic alterations cause functional changes in cell biology underlying cancer. These hallmark functional changes constitute potentially tissue-independent anticancer therapeutic targets. We hypothesized that RNA-Seq identifies ... ...

Abstract	Numerous genetic and epigenetic alterations cause functional changes in cell biology underlying cancer. These hallmark functional changes constitute potentially tissue-independent anticancer therapeutic targets. We hypothesized that RNA-Seq identifies gene expression changes that underly those hallmarks, and thereby defines relevant therapeutic targets. To test this hypothesis, we analysed the publicly available TCGA-TARGET-GTEx gene expression data set from the University of California Santa CruzToil recompute project using WGCNA to delineate co-correlated 'modules' from tumour gene expression profiles and functional enrichment of these modules to hierarchically cluster tumours. This stratified tumours according to T cell activation, NK-cell activation, complement cascade, ATM, Rb, angiogenic, MAPK, ECM receptor and histone modification signalling. These correspond to the cancer hallmarks of avoiding immune destruction, tumour-promoting inflammation, evading growth suppressors, inducing angiogenesis, sustained proliferative signalling, activating invasion and metastasis, and genome instability and mutation. This approach did not detect pathways corresponding to the cancer enabling replicative immortality, resisting cell death or deregulating cellular energetics hallmarks. We conclude that RNA-Seq stratifies tumours along some, but not all, hallmarks of cancer and, therefore, could be used in conjunction with other analyses collectively to inform precision therapy.
MeSH term(s)	Gene Expression Regulation, Neoplastic ; Humans ; Neoplasms/genetics ; Organ Specificity/genetics ; RNA-Seq ; Signal Transduction/genetics
Language	English
Publishing date	2019-11-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2074559-X
ISSN	1582-4934 ; 1582-4934 ; 1582-1838
ISSN (online)	1582-4934
ISSN	1582-4934 ; 1582-1838
DOI	10.1111/jcmm.14746
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Book: Thompson & Thompson genetics in medicine

Nussbaum, Robert L. / McInnes, Roderick R. / Willard, Huntington F. / Boerkoel, Cornelius F. / Thompson, James S. / Thompson, Margaret W.

2004

Title variant	Thompson and Thompson genetics in medicine ; Genetics in medicine
Author's details	Robert L. Nussbaum ; Roderick R. McInnes ; Huntington F. Willard. With clinical case studies prep. by Cornelius F. Boerkoel
Keywords	Genetics, Medical
Language	English
Size	XI, 444 S., [2] Bl. : Ill., graph. Darst., Kt.
Edition	6. ed., rev. reprint
Publisher	Saunders
Publishing place	Philadelphia, Pa
Publishing country	United States
Document type	Book
Old title	5. Aufl. u.d.T. Thompson, Margaret W.: Thompson & Thompson genetics in medicine
HBZ-ID	HT014160122
ISBN	0-7216-0244-4 ; 978-0-7216-0244-8
Database	Catalogue ZB MED Medicine, Health

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2004 A 4585	order for loan	Magazin
2005 A 6460	order for loan	Magazin

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Article ; Online: Generation of tandem alternative splice acceptor sites and CLTC haploinsufficiency: A cause of CLTC-related disorder.

Sage, Adam P / Lee, Hyun Kyung / Dalmann, Joshua / Lin, Susan / Samra, Simran / Salman, Areesha / Del Bel, Kate L / Li, Wenhui Laura / Lehman, Anna / Turvey, Stuart E / Boerkoel, Cornelius F / Richmond, Phillip A

American journal of medical genetics. Part A

2023 Volume 191, Issue 8, Page(s) 2219–2224

Abstract: Tandem splice acceptors ( ... ...

Abstract	Tandem splice acceptors (NAGN
MeSH term(s)	Humans ; RNA Splice Sites/genetics ; Haploinsufficiency/genetics ; Alternative Splicing/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Mutation ; Clathrin Heavy Chains/genetics
Chemical Substances	RNA Splice Sites ; RNA, Messenger ; CLTC protein, human ; Clathrin Heavy Chains (114899-12-6)
Language	English
Publishing date	2023-05-17
Publishing country	United States
Document type	Case Reports ; Research Support, Non-U.S. Gov't
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63249
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Article ; Online: Do PACS1 variants impeding adaptor protein binding predispose to syndromic intellectual disability?

Moller-Hansen, Ashley / Hejla, Duha / Lee, Hyun Kyung / Lyles, Jenea Barbara / Yang, Yunhan / Chen, Kun / Li, Wenhui Laura / Thomas, Gary / Boerkoel, Cornelius F

American journal of medical genetics. Part A

2023 Volume 191, Issue 8, Page(s) 2181–2187

Abstract: To date, PACS1-neurodevelopmental disorder (PACS1-NDD) has been associated with recurrent variation of Arg203 and is considered diagnostic of PACS1-NDD, an autosomal dominant syndromic intellectual disability disorder. Although incompletely defined, the ... ...

Abstract	To date, PACS1-neurodevelopmental disorder (PACS1-NDD) has been associated with recurrent variation of Arg203 and is considered diagnostic of PACS1-NDD, an autosomal dominant syndromic intellectual disability disorder. Although incompletely defined, the proposed disease mechanism for this variant is altered PACS1 affinity for its client proteins. Given this proposed mechanism, we hypothesized that PACS1 variants that interfere with binding of adaptor proteins might also give rise to syndromic intellectual disability. Herein, we report a proposita and her mother with phenotypic features overlapping PACS1-NDD and a novel PACS1 variant (NM_018026.3:c.[755C > T];[=], p.(Ser252Phe)) that impedes binding of the adaptor protein GGA3 (Golgi-associated, gamma-adaptin ear-containing, ARF-binding protein 3). We hypothesize that attenuating PACS1 binding of GGA3 also gives rise to a disorder with features overlapping those of PACS1-NDD. This observation better delineates the mechanism by which PACS1 variation predisposes to syndromic intellectual disability.
MeSH term(s)	Female ; Humans ; Intellectual Disability/diagnosis ; Intellectual Disability/genetics ; Neurodevelopmental Disorders ; Protein Binding ; Vesicular Transport Proteins/genetics
Chemical Substances	PACS1 protein, human ; Vesicular Transport Proteins ; GGA adaptor proteins
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Case Reports ; Research Support, N.I.H., Extramural
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63232
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Article: The role of nuclear bodies in gene expression and disease.

Morimoto, Marie / Boerkoel, Cornelius F

Biology

2013 Volume 2, Issue 3, Page(s) 976–1033

Abstract: This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, ... ...

Abstract	This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
Language	English
Publishing date	2013-08-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology2030976
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