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Article ; Online: Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease.

2024 Volume 56, Issue 3, Page(s) 420–430

Abstract: Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively ... ...

Abstract	Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells ; Heart Defects, Congenital/genetics ; Regulatory Sequences, Nucleic Acid ; Mutation ; Myocytes, Cardiac
Language	English
Publishing date	2024-02-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-024-01669-y
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Article ; Online: A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

Peters, Lauren A / Friedman, Joshua R / Stojmirovic, Aleksandar / Hagen, Jacob / Houten, Sander / Dodatko, Tetyana / Amaro, Mariana P / Restrepo, Paula / Chai, Zhi / Rodrigo Mora, J / Raymond, Holly A / Curran, Mark / Dobrin, Radu / Das, Anuk / Xiong, Huabao / Schadt, Eric E / Argmann, Carmen / Losic, Bojan

Communications biology

2023 Volume 6, Issue 1, Page(s) 95

Abstract: Previous studies have conducted time course characterization of murine colitis models through transcriptional profiling of differential expression. We characterize the transcriptional landscape of acute and chronic models of dextran sodium sulfate (DSS) ... ...

Abstract	Previous studies have conducted time course characterization of murine colitis models through transcriptional profiling of differential expression. We characterize the transcriptional landscape of acute and chronic models of dextran sodium sulfate (DSS) and adoptive transfer (AT) colitis to derive temporal gene expression and splicing signatures in blood and colonic tissue in order to capture dynamics of colitis remission and relapse. We identify sub networks of patient-derived causal networks that are enriched in these temporal signatures to distinguish acute and chronic disease components within the broader molecular landscape of IBD. The interaction between the DSS phenotype and chronological time-point naturally defines parsimonious temporal gene expression and splicing signatures associated with acute and chronic phases disease (as opposed to ordinary time-specific differential expression/splicing). We show these expression and splicing signatures are largely orthogonal, i.e. affect different genetic bodies, and that using machine learning, signatures are predictive of histopathological measures from both blood and intestinal data in murine colitis models as well as an independent cohort of IBD patients. Through access to longitudinal multi-scale profiling from disease tissue in IBD patient cohorts, we can apply this machine learning pipeline to generation of direct patient temporal multimodal regulatory signatures for prediction of histopathological outcomes.
MeSH term(s)	Animals ; Mice ; Inflammatory Bowel Diseases/genetics ; Colitis/chemically induced ; Colitis/genetics ; Phenotype ; Dextran Sulfate/toxicity
Chemical Substances	Dextran Sulfate (9042-14-2)
Language	English
Publishing date	2023-01-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-04469-y
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Article ; Online: Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas.

Zhong, Guojie / Ahimaz, Priyanka / Edwards, Nicole A / Hagen, Jacob J / Faure, Christophe / Lu, Qiao / Kingma, Paul / Middlesworth, William / Khlevner, Julie / El Fiky, Mahmoud / Schindel, David / Fialkowski, Elizabeth / Kashyap, Adhish / Forlenza, Sophia / Kenny, Alan P / Zorn, Aaron M / Shen, Yufeng / Chung, Wendy K

HGG advances

2022 Volume 3, Issue 3, Page(s) 100107

Abstract: Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare ... ...

Abstract	Esophageal atresias/tracheoesophageal fistulas (EA/TEF) are rare congenital anomalies caused by aberrant development of the foregut. Previous studies indicate that rare or
Language	English
Publishing date	2022-04-16
Publishing country	United States
Document type	Journal Article
ISSN	2666-2477
ISSN (online)	2666-2477
DOI	10.1016/j.xhgg.2022.100107
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Article ; Online: Erratum: Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas.

HGG advances

2022 Volume 3, Issue 3, Page(s) 100126

Abstract: This corrects the article DOI: 10.1016/j.xhgg.2022.100107.]. ...

Abstract	[This corrects the article DOI: 10.1016/j.xhgg.2022.100107.].
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Published Erratum
ISSN	2666-2477
ISSN (online)	2666-2477
DOI	10.1016/j.xhgg.2022.100126
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Article ; Online: Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma.

Ma, Mengqi / Ganapathi, Mythily / Zheng, Yiming / Tan, Kai-Li / Kanca, Oguz / Bove, Kevin E / Quintanilla, Norma / Sag, Sebnem O / Temel, Sehime G / LeDuc, Charles A / McPartland, Amanda J / Pereira, Elaine M / Shen, Yufeng / Hagen, Jacob / Thomas, Christie P / Galván, Nhu Thao Nguyen / Pan, Xueyang / Lu, Shenzhao / Rosenfeld, Jill A /

Calame, Daniel G / Wangler, Michael F / Lupski, James R / Pehlivan, Davut / Hertel, Paula M / Chung, Wendy K / Bellen, Hugo J

Genetics in medicine : official journal of the American College of Medical Genetics

2024 , Page(s) 101125

Abstract: Purpose: YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases.: Methods: We report three unrelated individuals with rare homozygous missense variants in YKT6 who exhibited ...

Abstract	Purpose: YKT6 plays important roles in multiple intracellular vesicle trafficking events but has not been associated with Mendelian diseases. Methods: We report three unrelated individuals with rare homozygous missense variants in YKT6 who exhibited neurological disease with or without a progressive infantile liver disease. We modeled the variants in Drosophila. We generated wild-type and variant genomic rescue constructs (GRs) of the fly ortholog dYkt6 and compared their ability in rescuing the loss-of-function phenotypes in mutant flies. We also generated a dYkt6 Results: Two individuals are homozygous for YKT6 [NM_006555.3:c.554A>G p.(Tyr185Cys)] and exhibited normal prenatal course followed by failure to thrive, developmental delay and progressive liver disease. Haplotype analysis identified a shared homozygous region flanking the variant, suggesting a common ancestry. The third individual is homozygous for YKT6 [NM_006555.3:c.191A>G p.(Tyr64Cys)] and exhibited neurodevelopmental disorders and optic atrophy. Fly dYkt6 is essential and is expressed in the fat body (analogous to liver) and central nervous system. Wild-type GR can rescue the lethality and autophagic flux defects whereas the variants are less efficient in rescuing the phenotypes. Conclusion: The YKT6 variants are partial loss-of-function alleles and the p.(Tyr185Cys) is more severe than p.(Tyr64Cys).
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1455352-1
ISSN	1530-0366 ; 1098-3600
ISSN (online)	1530-0366
ISSN	1098-3600
DOI	10.1016/j.gim.2024.101125
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Article ; Online: A disorder-related variant (E420K) of a PP2A-regulatory subunit (PPP2R5D) causes constitutively active AKT-mTOR signaling and uncoordinated cell growth.

Papke, Cinta M / Smolen, Kali A / Swingle, Mark R / Cressey, Lauren / Heng, Richard A / Toporsian, Mourad / Deng, Liyong / Hagen, Jacob / Shen, Yufeng / Chung, Wendy K / Kettenbach, Arminja N / Honkanen, Richard E

The Journal of biological chemistry

2021 Volume 296, Page(s) 100313

Abstract: Functional genomic approaches have facilitated the discovery of rare genetic disorders and improved efforts to decipher their underlying etiology. PPP2R5D-related disorder is an early childhood onset condition characterized by intellectual disability, ... ...

Abstract	Functional genomic approaches have facilitated the discovery of rare genetic disorders and improved efforts to decipher their underlying etiology. PPP2R5D-related disorder is an early childhood onset condition characterized by intellectual disability, hypotonia, autism-spectrum disorder, macrocephaly, and dysmorphic features. The disorder is caused by de novo single nucleotide changes in PPP2R5D, which generate heterozygous dominant missense variants. PPP2R5D is known to encode a B'-type (B'56δ) regulatory subunit of a PP2A-serine/threonine phosphatase. To help elucidate the molecular mechanisms altered in PPP2R5D-related disorder, we used a CRISPR-single-base editor to generate HEK-293 cells in which a single transition (c.1258G>A) was introduced into one allele, precisely recapitulating a clinically relevant E420K variant. Unbiased quantitative proteomic and phosphoproteomic analyses of endogenously expressed proteins revealed heterozygous-dominant changes in kinase/phosphatase signaling. These data combined with orthogonal validation studies revealed a previously unrecognized interaction of PPP2R5D with AKT in human cells, leading to constitutively active AKT-mTOR signaling, increased cell size, and uncoordinated cellular growth in E420K-variant cells. Rapamycin reduced cell size and dose-dependently reduced RPS6 phosphorylation in E420K-variant cells, suggesting that inhibition of mTOR1 can suppress both the observed RPS6 hyperphosphorylation and increased cell size. Together, our findings provide a deeper understanding of PPP2R5D and insight into how the E420K-variant alters signaling networks influenced by PPP2R5D. Our comprehensive approach, which combines precise genome editing, isobaric tandem mass tag labeling of peptides generated from endogenously expressed proteins, and concurrent liquid chromatography-mass spectrometry (LC-MS
MeSH term(s)	Autistic Disorder/genetics ; Autistic Disorder/pathology ; CRISPR-Cas Systems/genetics ; Genetic Diseases, Inborn/genetics ; Genetic Diseases, Inborn/pathology ; Genetic Predisposition to Disease ; Humans ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Megalencephaly/genetics ; Megalencephaly/pathology ; Mutation/genetics ; Polymorphism, Single Nucleotide/genetics ; Protein Phosphatase 2/genetics ; Proteomics ; Proto-Oncogene Proteins c-akt/genetics ; TOR Serine-Threonine Kinases/genetics
Chemical Substances	PPP2R5D protein, human ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Protein Phosphatase 2 (EC 3.1.3.16)
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100313
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Article ; Online: Bi-allelic PAGR1 variants are associated with microcephaly and a severe neurodevelopmental disorder: Genetic evidence from two families.

Daum, Hagit / Ganapathi, Mythily / Hirsch, Yoel / Griffin, Emily L / LeDuc, Charles A / Hagen, Jacob / Yagel, Simcha / Meiner, Vardiella / Chung, Wendy K / Mor-Shaked, Hagar

American journal of medical genetics. Part A

2021 Volume 188, Issue 1, Page(s) 336–342

Abstract: Exome and genome sequencing were used to identify the genetic etiology of a severe neurodevelopmental disorder in two unrelated Ashkenazi Jewish families with three affected individuals. The clinical findings included a prenatal presentation of ... ...

Abstract	Exome and genome sequencing were used to identify the genetic etiology of a severe neurodevelopmental disorder in two unrelated Ashkenazi Jewish families with three affected individuals. The clinical findings included a prenatal presentation of microcephaly, polyhydramnios and clenched hands while postnatal findings included microcephaly, severe developmental delay, dysmorphism, neurologic deficits, and death in infancy. A shared rare homozygous, missense variant (c.274A > G; p.Ser92Gly, NM_024516.4) was identified in PAGR1, a gene currently not associated with a Mendelian disease. PAGR1 encodes a component of the histone methyltransferase MLL2/MLL3 complex and may function in the DNA damage response pathway. Complete knockout of the murine Pagr1a is embryonic-lethal. Given the available evidence, PAGR1 is a strong candidate gene for a novel autosomal recessive severe syndromic neurodevelopmental disorder.
MeSH term(s)	Alleles ; Animals ; Cell Cycle Proteins/genetics ; DNA-Binding Proteins/genetics ; Exome/genetics ; Humans ; Mice ; Microcephaly/genetics ; Nervous System Malformations/genetics ; Neurodevelopmental Disorders/genetics ; Pedigree
Chemical Substances	Cell Cycle Proteins ; DNA-Binding Proteins ; PAGR1 protein, human
Language	English
Publishing date	2021-09-29
Publishing country	United States
Document type	Case Reports ; Research Support, N.I.H., Extramural ; 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.62513
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Article ; Online: Tissue specific expression of myosin IC isoforms.

Sielski, Neil L / Ihnatovych, Ivanna / Hagen, Jacob J / Hofmann, Wilma A

BMC cell biology

2014 Volume 15, Page(s) 8

Abstract: Background: Myosin IC is a single headed member of the myosin superfamily that localizes to the cytoplasm and the nucleus and is implicated in a variety of processes in both compartments. We recently identified a novel isoform of myosin IC and showed ... ...

Abstract	Background: Myosin IC is a single headed member of the myosin superfamily that localizes to the cytoplasm and the nucleus and is implicated in a variety of processes in both compartments. We recently identified a novel isoform of myosin IC and showed that the MYOIC gene in mammalian cells encodes three isoforms (isoforms A, B, and C) that differ only in the addition of short isoform-specific N-terminal peptides. The expression pattern of the isoforms and the mechanisms of expression regulation remain unknown. Results: To determine the expression patterns of myosin IC isoforms, we performed a comprehensive expression analysis of the two myosin IC isoforms (isoform A and B) that contain isoform-specific sequences. By immunoblotting with isoform-specific antibodies and by qRT-PCR with isoform-specific primer we demonstrate that myosin IC isoforms A and B have distinct expression patterns in mouse tissues. Specifically, we show that myosin IC isoform A is expressed in a tissue specific pattern, while myosin IC isoform B is ubiquitously expressed at comparable levels in mouse tissues. Conclusions: The differences in the expression profile of the myosin IC isoforms indicate a tissue-specific MYOIC gene regulation and further suggest that the myosin IC isoforms, despite their high sequence homology, might have tissue-specific and isoform-specific functions.
MeSH term(s)	Animals ; Blotting, Western ; Female ; Gene Expression Regulation ; Male ; Mice ; Mice, Inbred C57BL ; Myosins/genetics ; Myosins/metabolism ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; RNA, Messenger/metabolism ; Real-Time Polymerase Chain Reaction
Chemical Substances	Protein Isoforms ; RNA, Messenger ; Myosins (EC 3.6.4.1)
Language	English
Publishing date	2014-03-11
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1471-2121
ISSN (online)	1471-2121
DOI	10.1186/1471-2121-15-8
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Article: Evaluation of leg banding and attachment of radio-transmitters on ring-necked pheasant chicks

Carroll, J. Matthew / Hamm, R. Lee / Hagen, Jacob M. / Davis, Craig A. / Guthery, Fred S.

Wildlife biology. 2017, v. 2017, no. 4

2017

Abstract: Marking birds is a vital tool for determining survival, habitat-use patterns, and movements. For galliform species, metal leg bands and radio-transmitters are widely used marking techniques. While commonly used on adult birds, leg banding and radio- ... ...

Abstract	Marking birds is a vital tool for determining survival, habitat-use patterns, and movements. For galliform species, metal leg bands and radio-transmitters are widely used marking techniques. While commonly used on adult birds, leg banding and radio-marking of galliform chicks are not commonly employed. During a two-year study to evaluate survival, dispersal, and habitat-use of released four-week old ring-necked pheasants Phasianus colchicus, we sought to mark chicks in a manner that allowed us to track them post-release and recognize them if harvested as adults. Our objectives were to evaluate the efficacy of four banding techniques: 1) standard bands for adult ring-necked pheasants [no. 6 aluminum butt-end bands], 2) colored plastic spiral leg bands commonly used for banding poultry, 3) no. 6 bands and plastic spiral leg bands to prevent the aluminum bands from slipping off, and 4) cotton-filled no. 6 bands to prevent bands from slipping off and allow growth of the tarsus. We also evaluated two radio-transmitter attachment methods: gluing or suturing transmitters on the back of four-week-old chicks. The no. 6 bands did not stay attached to the birds due to the bands being too large, and plastic spiral bands commonly caused constriction of the legs, possibly crippling birds. However, using cotton filled leg-bands was a reliable method for marking pheasant chicks. Although gluing has been used successfully as a radio-transmitter attachment method in other studies, in our study it largely failed given that few radio-transmitters remained attached beyond two days. Suturing was an effective method (90% of the transmitters remained attached until death or expected life of the battery) for attaching radio-transmitters to ring-necked pheasant chicks. Our field study has revealed promising approaches and we suggest that a captive study should now evaluate the possible sub-lethal effects (e.g. growth rates, body condition, transmitter retention times) of these attachment methods.
Keywords	Phasianus colchicus ; adults ; aluminum ; batteries ; body condition ; cotton ; death ; pheasants ; radio transmitters ; wildlife
Language	English
Publishing place	Nordic Board for Wildlife Research
Document type	Article
ZDB-ID	1291831-3
ISSN	0909-6396
ISSN	0909-6396
DOI	10.2981/wlb.00263
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A novel homozygous variant in

Al-Deri, Noraldin / Okur, Volkan / Ahimaz, Priyanka / Milev, Miroslav / Valivullah, Zaheer / Hagen, Jacob / Sheng, Yufeng / Chung, Wendy / Sacher, Michael / Ganapathi, Mythily

Journal of medical genetics

2020 Volume 58, Issue 9, Page(s) 592–601

Abstract: Background: Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in : Methods: We performed whole genome ... ...

Abstract	Background: Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in Methods: We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified Results: A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in Conclusion: Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the
MeSH term(s)	Adult ; Age of Onset ; Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; DNA Mutational Analysis ; Female ; Genetic Association Studies ; Genetic Predisposition to Disease ; Haplotypes ; Homozygote ; Humans ; Male ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/genetics ; Mutation ; Neurodevelopmental Disorders/diagnosis ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/metabolism ; Pedigree ; Phenotype ; Protein Binding ; Protein Multimerization ; Structure-Activity Relationship ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Vesicular Transport Proteins/chemistry ; Vesicular Transport Proteins/metabolism
Chemical Substances	Membrane Transport Proteins ; TRAPPC2 protein, human ; Transcription Factors ; Vesicular Transport Proteins ; transport protein particle, TRAPP
Language	English
Publishing date	2020-08-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	220881-7
ISSN	1468-6244 ; 0022-2593
ISSN (online)	1468-6244
ISSN	0022-2593
DOI	10.1136/jmedgenet-2020-107016
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