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Potter SJ, Zhang L, Kotliar M, Wu Y, Schafer C, Stefan K, Boukas L, Qu’d D, Bodamer O, Simpson BN, Barski A, Lindsley AW, Bjornsson HT. KMT2D regulates activation, localization, and integrin expression by T-cells. Front Immunol 2024; 15:1341745. [PMID: 38765012 PMCID: PMC11099208 DOI: 10.3389/fimmu.2024.1341745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 05/21/2024] Open
Abstract
Individuals with Kabuki syndrome present with immunodeficiency; however, how pathogenic variants in the gene encoding the histone-modifying enzyme lysine methyltransferase 2D (KMT2D) lead to immune alterations remain poorly understood. Following up on our prior report of KMT2D-altered integrin expression in B-cells, we performed targeted analyses of KMT2D's influence on integrin expression in T-cells throughout development (thymocytes through peripheral T-cells) in murine cells with constitutive- and conditional-targeted Kmt2d deletion. Using high-throughput RNA-sequencing and flow cytometry, we reveal decreased expression (both at the transcriptional and translational levels) of a cluster of leukocyte-specific integrins, which perturb aspects of T-cell activation, maturation, adhesion/localization, and effector function. H3K4me3 ChIP-PCR suggests that these evolutionary similar integrins are under direct control of KMT2D. KMT2D loss also alters multiple downstream programming/signaling pathways, including integrin-based localization, which can influence T-cell populations. We further demonstrated that KMT2D deficiency is associated with the accumulation of murine CD8+ single-positive (SP) thymocytes and shifts in both human and murine peripheral T-cell populations, including the reduction of the CD4+ recent thymic emigrant (RTE) population. Together, these data show that the targeted loss of Kmt2d in the T-cell lineage recapitulates several distinct features of Kabuki syndrome-associated immune deficiency and implicates epigenetic mechanisms in the regulation of integrin signaling.
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Affiliation(s)
- Sarah J. Potter
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Li Zhang
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael Kotliar
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Yuehong Wu
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Caitlin Schafer
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Leandros Boukas
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dima Qu’d
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
- The Roya Kabuki Program, Boston Children’s Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Broad Institute of MIT and Harvard University, Cambridge, MA, United States
| | - Brittany N. Simpson
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew W. Lindsley
- Division of Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Hans T. Bjornsson
- McKusick-Nathans Department of Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Faculty of Medicine, The University of Iceland, Reykjavik, Iceland
- Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
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Harris JR, Gao CW, Britton JF, Applegate CD, Bjornsson HT, Fahrner JA. Five years of experience in the Epigenetics and Chromatin Clinic: what have we learned and where do we go from here? Hum Genet 2024; 143:607-624. [PMID: 36952035 PMCID: PMC10034257 DOI: 10.1007/s00439-023-02537-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/20/2023] [Indexed: 03/24/2023]
Abstract
The multidisciplinary Epigenetics and Chromatin Clinic at Johns Hopkins provides comprehensive medical care for individuals with rare disorders that involve disrupted epigenetics. Initially centered on classical imprinting disorders, the focus shifted to the rapidly emerging group of genetic disorders resulting from pathogenic germline variants in epigenetic machinery genes. These are collectively called the Mendelian disorders of the epigenetic machinery (MDEMs), or more broadly, Chromatinopathies. In five years, 741 clinic visits have been completed for 432 individual patients, with 153 having confirmed epigenetic diagnoses. Of these, 115 individuals have one of 26 MDEMs with every single one exhibiting global developmental delay and/or intellectual disability. This supports prior observations that intellectual disability is the most common phenotypic feature of MDEMs. Additional common phenotypes in our clinic include growth abnormalities and neurodevelopmental issues, particularly hypotonia, attention-deficit/hyperactivity disorder (ADHD), and anxiety, with seizures and autism being less common. Overall, our patient population is representative of the broader group of MDEMs and includes mostly autosomal dominant disorders impacting writers more so than erasers, readers, and remodelers of chromatin marks. There is an increased representation of dual function components with a reader and an enzymatic domain. As expected, diagnoses were made mostly by sequencing but were aided in some cases by DNA methylation profiling. Our clinic has helped to facilitate the discovery of two new disorders, and our providers are actively developing and implementing novel therapeutic strategies for MDEMs. These data and our high follow-up rate of over 60% suggest that we are achieving our mission to diagnose, learn from, and provide optimal care for our patients with disrupted epigenetics.
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Affiliation(s)
- Jacqueline R Harris
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Kennedy Krieger Institute, Baltimore, MD, USA
| | - Christine W Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Johns Hopkins Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacquelyn F Britton
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carolyn D Applegate
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Enkhmandakh B, Robson P, Joshi P, Vijaykumar A, Shin DG, Mina M, Bayarsaihan D. Single-Cell Transcriptome Analysis Defines Expression of Kabuki Syndrome-Associated KMT2D Targets and Interacting Partners. Stem Cells Int 2022; 2022:4969441. [PMID: 35992033 PMCID: PMC9391158 DOI: 10.1155/2022/4969441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 07/30/2022] [Indexed: 11/18/2022] Open
Abstract
Objectives. Kabuki syndrome (KS) is a rare genetic disorder characterized by developmental delay, retarded growth, and cardiac, gastrointestinal, neurocognitive, renal, craniofacial, dental, and skeletal defects. KS is caused by mutations in the genes encoding histone H3 lysine 4 methyltransferase (KMT2D) and histone H3 lysine 27 demethylase (KDM6A), which are core components of the complex of proteins associated with histone H3 lysine 4 methyltransferase SET1 (SET1/COMPASS). Using single-cell RNA data, we examined the expression profiles of Kmt2d and Kdm6a in the mouse dental pulp. In the incisor pulp, Kmt2d and Kdm6a colocalize with other genes of the SET1/COMPASS complex comprised of the WD-repeat protein 5 gene (Wdr5), the retinoblastoma-binding protein 5 gene (Rbbp5), absent, small, and homeotic 2-like protein-encoding gene (Ash2l), nuclear receptor cofactor 6 gene (Ncoa6), and Pax-interacting protein 1 gene (Ptip1). In addition, we found that Kmt2d and Kdm6a coexpress with the downstream target genes of the Wingless and Integrated (WNT) and sonic hedgehog signaling pathways in mesenchymal stem/stromal cells (MSCs) at different stages of osteogenic differentiation. Taken together, our results suggest an essential role of KMT2D and KDK6A in directing lineage-specific gene expression during differentiation of MSCs.
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Affiliation(s)
- Badam Enkhmandakh
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Anushree Vijaykumar
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Mina Mina
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
- Institute for System Genomics, University of Connecticut, Engineering Science Building Rm. 305, 67 North Eagleville Road, Storrs, CT 06269, USA
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Gooch C, Souder JP, Tedder ML, Kerkhof J, Lee JA, Louie RJ, Sadikovic B, Fletcher RS, Robin NH. Near complete deletion of KMT2D in a college student. Am J Med Genet A 2022; 188:1550-1555. [PMID: 35040536 PMCID: PMC8995339 DOI: 10.1002/ajmg.a.62652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/09/2022]
Abstract
Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.
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Affiliation(s)
- Catherine Gooch
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jaclyn Paige Souder
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | | | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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