1
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Michelson M, Yosovich K, Bahar S, Yogev Y, Birk OS, Ginzberg M, Lev D. Novel phenotype associated with homozygous likely pathogenic variant in the POP1 gene. Clin Genet 2024; 105:671-675. [PMID: 38351533 DOI: 10.1111/cge.14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
The biallelic variants of the POP1 gene are associated with the anauxetic dysplasia (AAD OMIM 607095), a rare skeletal dysplasia, characterized by prenatal rhizomelic shortening of limbs and generalized joint hypermobility. Affected individuals usually have normal neurodevelopmental milestones. Here we present three cases from the same family with likely pathogenic homozygous POP1 variant and a completely novel phenotype: a girl with global developmental delay and autism, microcephaly, peculiar dysmorphic features and multiple congenital anomalies. Two subsequent pregnancies were terminated due to multiple congenital malformations. Fetal DNA samples revealed the same homozygous variant in the POP1 gene. Expression of the RMRP was reduced in the proband compared with control and slightly reduced in both heterozygous parents, carriers for this variant. To our knowledge, this is the first report of this new phenotype, associated with a novel likely pathogenic variant in POP1. Our findings expand the phenotypic spectrum of POP1-related disorders.
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Affiliation(s)
- Marina Michelson
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
- The Genetic Institute of Maccabi Health Medicinal Organization, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Keren Yosovich
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Sarit Bahar
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Genetics Institute, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Mira Ginzberg
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
- The Genetic Institute of Maccabi Health Medicinal Organization, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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2
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Dynamic enhancer landscapes in human craniofacial development. Nat Commun 2024; 15:2030. [PMID: 38448444 PMCID: PMC10917818 DOI: 10.1038/s41467-024-46396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Laura E Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Cailyn H Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, 3010, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Lucile Packard Children's Hospital, Stanford University, Stanford, CA, 94304, USA
| | - Matthew J Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA, 94110, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Octant Inc., Emeryville, CA, 94608, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- School of Natural Sciences, University of California, Merced, CA, USA.
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3
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Travessa AM, Dias P, Rosmaninho-Salgado J, Aza-Carmona M, Moldovan O, Díaz-González F, Godinho F, Romeu JC, Oliveira-Ramos F, do Céu Barreiros M, Sousa SB, Heath KE, Sousa AB. Characterization of three adults and an adolescent with Osteogenesis Imperfecta type VI and a novel founder SERPINF1 variant. Eur J Med Genet 2023; 66:104867. [PMID: 37839784 DOI: 10.1016/j.ejmg.2023.104867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/17/2023]
Abstract
Osteogenesis imperfecta (OI) type VI is an extremely rare form of OI caused by biallelic variants in the SERPINF1 gene, which codes for the pigment-epithelium derived factor (PEDF). We report on four patients (three adults and one adolescent) with a severe deforming form of OI. All patients presented no abnormalities at birth, frequent long bone and vertebrae fractures (mainly during childhood), marked short stature, severe bone deformities, chronic mild to moderate pain, and severe limitation of mobility, with three being completely wheelchair bound. Blue sclera and dentinogenesis imperfecta were absent, although some patients presented tooth, ophthalmological, and/or cardiac features. Radiographic findings included, among others, thin diaphysis and popcorn calcifications, both of which are non-specific to this type of OI. The novel homozygous variants c.816_819del (p.Met272Ilefs*8) and c.283+2T > G in SERPINF1 were identified in three and one patient, respectively. The three patients carrying the frameshift variant were born in nearby regions suggesting a founder effect. Describing the long-term outcomes of four patients with OI type VI, this cohort adds relevant data on the clinical features and prognosis of this type of OI.
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Affiliation(s)
- André M Travessa
- Medical Genetics Department and ERN-BOND, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal; Institute of Histology and Developmental Biology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal.
| | - Patrícia Dias
- Medical Genetics Department and ERN-BOND, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Joana Rosmaninho-Salgado
- Medical Genetics Unit and ERN-BOND, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Miriam Aza-Carmona
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain; Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Oana Moldovan
- Medical Genetics Department and ERN-BOND, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Francisca Díaz-González
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain; Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Fátima Godinho
- Department of Rheumatology, Hospital Garcia de Orta, Almada, Portugal; Associação Portuguesa de Osteogénese Imperfeita (APOI), Lisbon, Portugal
| | - José Carlos Romeu
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Filipa Oliveira-Ramos
- Rheumatology Research Unit, Molecular Medicine Institute, Faculty of Medicine, University of Lisbon, Lisbon, Portugal; Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | | | - Sérgio B Sousa
- Medical Genetics Unit and ERN-BOND, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Karen E Heath
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain; Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Ana Berta Sousa
- Medical Genetics Department and ERN-BOND, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal; Rheumatology Research Unit, Molecular Medicine Institute, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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4
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Remmelzwaal PC, Verhagen MV, Jongbloed JDH, van den Akker PC, Veenstra-Knol HE, Hitzert MM. Expanding the phenotype of anauxetic dysplasia caused by biallelic NEPRO mutations: A case report. Am J Med Genet A 2023; 191:2440-2445. [PMID: 37294112 DOI: 10.1002/ajmg.a.63316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
The cartilage hair hypoplasia and anauxetic dysplasia (CHH-AD) spectrum encompasses a group of rare skeletal disorders, with anauxetic dysplasia (ANXD) at the most severe end of the spectrum. Biallelic variants in RMRP, POP1, and NEPRO (C3orf17) have previously been associated with the three currently recognized ANXD types. Generally, all types are characterized by severe short stature, brachydactyly, skin laxity, joint hypermobility and dislocations, and extensive skeletal abnormalities visible on radiological evaluation. Thus far, only five patients with type 3 anauxetic dysplasia (ANXD3) have been reported. Here, we describe one additional ANXD3 patient. We provide a detailed physical and radiological evaluation of this patient, in whom we identified a homozygous variant, c.280C > T, p.(Arg94Cys), in NEPRO. Our patient presented with clinically relevant features not previously described in ANXD3: atlantoaxial subluxation, extensive dental anomalies, and a sagittal suture craniosynostosis resulting in scaphocephaly. We provide an overview of the literature on ANXD3 and discuss our patient's characteristics in the context of previously described patients. This study expands the phenotypic spectrum of ANXD, particularly ANXD3. Greater awareness of the possibility of atlantoaxial subluxation, dental anomalies, and craniosynostosis may lead to more timely diagnosis and treatment.
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Affiliation(s)
- P Christian Remmelzwaal
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martijn V Verhagen
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter C van den Akker
- Department of Genetics, Groningen Expertise Center for Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marrit M Hitzert
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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5
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Schneider C, Bohnsack KE. Caught in the act-Visualizing ribonucleases during eukaryotic ribosome assembly. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1766. [PMID: 36254602 DOI: 10.1002/wrna.1766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 07/20/2023]
Abstract
Ribosomes are essential macromolecular machines responsible for translating the genetic information encoded in mRNAs into proteins. Ribosomes are composed of ribosomal RNAs and proteins (rRNAs and RPs) and the rRNAs fulfill both catalytic and architectural functions. Excision of the mature eukaryotic rRNAs from their precursor transcript is achieved through a complex series of endoribonucleolytic cleavages and exoribonucleolytic processing steps that are precisely coordinated with other aspects of ribosome assembly. Many ribonucleases involved in pre-rRNA processing have been identified and pre-rRNA processing pathways are relatively well defined. However, momentous advances in cryo-electron microscopy have recently enabled structural snapshots of various pre-ribosomal particles from budding yeast (Saccharomyces cerevisiae) and human cells to be captured and, excitingly, these structures not only allow pre-rRNAs to be observed before and after cleavage events, but also enable ribonucleases to be visualized on their target RNAs. These structural views of pre-rRNA processing in action allow a new layer of understanding of rRNA maturation and how it is coordinated with other aspects of ribosome assembly. They illuminate mechanisms of target recognition by the diverse ribonucleases involved and reveal how the cleavage/processing activities of these enzymes are regulated. In this review, we discuss the new insights into pre-rRNA processing gained by structural analyses and the growing understanding of the mechanisms of ribonuclease regulation. This article is categorized under: Translation > Ribosome Biogenesis RNA Processing > rRNA Processing.
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Affiliation(s)
- Claudia Schneider
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
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6
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Rajderkar SS, Paraiso K, Amaral ML, Kosicki M, Cook LE, Darbellay F, Spurrell CH, Osterwalder M, Zhu Y, Wu H, Afzal SY, Blow MJ, Kelman G, Barozzi I, Fukuda-Yuzawa Y, Akiyama JA, Afzal V, Tran S, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Wang A, Lin L, Preissl S, Lisgo S, Ren B, Dickel DE, Pennacchio LA, Visel A. Cell Type- and Tissue-specific Enhancers in Craniofacial Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546603. [PMID: 37425964 PMCID: PMC10327103 DOI: 10.1101/2023.06.26.546603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development1-3. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined histone modification and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. We used transgenic mouse reporter assays to determine the in vivo activity patterns of human face enhancers predicted from these data. Across 16 in vivo validated human enhancers, we observed a rich diversity of craniofacial subregions in which these enhancers are active in vivo. To annotate the cell type specificities of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating these data across species, we find that the majority (56%) of human craniofacial enhancers are functionally conserved in mice, providing cell type- and embryonic stage-resolved predictions of their in vivo activity profiles. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we demonstrate the utility of these data for predicting the in vivo cell type specificity of enhancers. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.
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Affiliation(s)
- Sudha Sunil Rajderkar
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Kitt Paraiso
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Laura E. Cook
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Fabrice Darbellay
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Cailyn H. Spurrell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Marco Osterwalder
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Han Wu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sarah Yasmeen Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Lucile Packard Children’s Hospital, Stanford University, Stanford, CA 94304
| | - Matthew J. Blow
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Guy Kelman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- The Jerusalem Center for Personalized Computational Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Iros Barozzi
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Yoko Fukuda-Yuzawa
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- University Research Management Center, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Jennifer A. Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S. Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Riana D. Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- UC San Francisco, Division of Experimental Medicine, 1001 Potrero Ave, San Francisco, CA 94110
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Bing Ren
- Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Diane E. Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Octant Inc., Emeryville, CA 94608, USA
| | - Len A. Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, California, USA
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7
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Del Pino M, Huckstadt V, Diaz-Gonzalez F, Obregon MG, Heath KE, Fano V. Clinical and radiological heterogeneity for the rare FGFR3 variant, p.Ser344Cys, description of a third patient. Am J Med Genet A 2023. [PMID: 37128991 DOI: 10.1002/ajmg.a.63227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Mariana Del Pino
- Growth and Development, Hospital Garrahan, Buenos Aires, Argentina
| | | | - Francisca Diaz-Gonzalez
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, UAM, IdiPAZ, Madrid, Spain
- Skeletal Dysplasia Multidisciplinary Unit (UMDE-ERN BOND), Hospital Universitario La Paz, UAM, Madrid, Spain
| | | | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, UAM, IdiPAZ, Madrid, Spain
- Skeletal Dysplasia Multidisciplinary Unit (UMDE-ERN BOND), Hospital Universitario La Paz, UAM, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Virginia Fano
- Growth and Development, Hospital Garrahan, Buenos Aires, Argentina
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8
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Lorenzo C, Travessa AM, Ferreira AC, Modamio-Høybjør S, Heath KE, Pereira C. Precocious puberty and anal stenosis in an African patient with Rothmund-Thomson syndrome. Am J Med Genet A 2023; 191:280-283. [PMID: 36164748 DOI: 10.1002/ajmg.a.62980] [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: 06/01/2022] [Revised: 08/14/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022]
Abstract
Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive disorder characterized by a rash that progresses to poikiloderma. Other common features include sparse hair, eyelashes and eyebrows, short stature, variable skeletal abnormalities, dental defects, cataracts, hypogonadism, and an increased risk for cancer, especially osteosarcoma and skin cancer. RTS is caused by biallelic pathogenic variants in ANAPC1 (Type 1 RTS) or RECQL4 (Type 2 RTS). We present an African girl with Type 2 RTS caused by a nonsense variant and an intronic variant in RECQL4. The patient presented precocious puberty, which has not been previously reported in RTS and that was treated with a GnRH analog, and anal stenosis, which has only been reported once. This case highlights the need to consider deep intronic variants in patients with RTS when pathogenic variants in the coding regions and exon/intron boundaries are not identified and expands the phenotypic spectrum of this disorder.
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Affiliation(s)
- Cristina Lorenzo
- Department of Pediatrics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, EPE, Lisbon, Portugal
| | - André M Travessa
- Medical Genetics Department and ERN-BOND, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, EPE, Lisbon, Portugal.,Faculty of Medicine, Institute of Histology and Developmental Biology, University of Lisbon, Lisbon, Portugal
| | - Ana Cristóvão Ferreira
- Department of Pediatrics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, EPE, Lisbon, Portugal
| | - Silvia Modamio-Høybjør
- Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, La Paz University Hospital, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain
| | - Karen E Heath
- Skeletal Dysplasia Multidisciplinary Unit (UMDE) and ERN-BOND, La Paz University Hospital, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain
| | - Carla Pereira
- Pediatric Endocrinology Unit, Department of Pediatrics, Hospital de Santa Maria - Centro Hospitalar Universitário Lisboa Norte, EPE, Lisbon, Portugal
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9
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Robertson N, Shchepachev V, Wright D, Turowski TW, Spanos C, Helwak A, Zamoyska R, Tollervey D. A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis. Nat Commun 2022; 13:649. [PMID: 35115551 PMCID: PMC8814244 DOI: 10.1038/s41467-022-28295-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 01/14/2022] [Indexed: 01/02/2023] Open
Abstract
RMRP encodes a non-coding RNA forming the core of the RNase MRP ribonucleoprotein complex. Mutations cause Cartilage Hair Hypoplasia (CHH), characterized by skeletal abnormalities and impaired T cell activation. Yeast RNase MRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Patient-derived human fibroblasts with CHH-linked mutations showed similar pre-rRNA processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy.
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Affiliation(s)
- Nic Robertson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vadim Shchepachev
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - David Wright
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aleksandra Helwak
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Rose Zamoyska
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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10
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Liu Y, Sun H, Li X, Liu Q, Zhao Y, Li L, Xu B, Hou Y, Jin W. Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer. Front Oncol 2021; 11:663556. [PMID: 34322380 PMCID: PMC8311660 DOI: 10.3389/fonc.2021.663556] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/19/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND To date, breast cancer remains the primary cause of tumor-related death among women, even though some leap-type developments of oncology have been done to slash the mortality. Considering the tumor heterogeneity and individual variation, the more reliable biomarkers are required to be identified for supporting the development of precision medicine in breast cancer. METHODS Based on the TCGA-BRCA and METABRIC databases, the differently expressed RNA binding proteins (RBPs) between tumor and normal tissues were investigated. In this study, we focused on the communal differently expressed RBPs in four subtypes of breast cancer. Lasso-penalized Cox analysis, Stepwise-multivariate Cox analysis and Kaplan-Meier survival curve were performed to identify the hub RBP-coding genes in predicting prognosis of breast cancer, and a prognostic model was established. The efficiency of this model was further validated in other independent GSE20685, GSE4922 and FUSCC-TNBC cohorts by calculating the risk score and performing survival analysis, ROC and nomogram. Moreover, pathologic functions of the candidate RBPs in breast cancer were explored using some routine experiments in vitro, and the potential compounds targeting these RBPs were predicted by reviewing the Comparative Toxicogenomics Database. RESULTS Here, we identified 62 RBPs which were differently expressed between the tumor and normal tissues. Thereinto, three RBPs (MRPL12, MRPL13 and POP1) acted as independent risk factors, and their expression pattern also correlated with poor prognosis of patients. A prognostic model, built with these 3-RBPs, possessed statistical significance to predict the survival probability of patients with breast cancer. Furthermore, experimental validations showed that down-regulating the expression of endogenous MRPL12, MRPL13 or POP1 could dramatically suppress the cellular viability and migration of breast cancer cells in vitro. Besides, some compounds (such as the Acetaminophen, Urethane and Tunicamycin) were predicted for curing breast cancer via targeting MRPL12, MRPL13 and POP1 simultaneously. CONCLUSION This study identified and established a 3-RBPs-based signature and nomogram for predicting the survival probability of patients with breast cancer. MRPL12, MRPL13 and POP1 might act as oncogenes in maintaining cellular viability and accelerating metastasis of breast cancer cells, implying the possibility of which to be designed as biomarkers and/or therapeutic targets for breast cancer.
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Affiliation(s)
- Yang Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hefen Sun
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xuan Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiqi Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuanyuan Zhao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liangdong Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Baojin Xu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yifeng Hou
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Jin
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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11
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Travessa AM, Díaz-González F, Mirco T, Oliveira-Ramos F, Parrón-Pajares M, Heath KE, Sousa AB. Spondyloepiphyseal dysplasia type Stanescu: Expanding the clinical and molecular spectrum of a very rare type II collagenopathy. Am J Med Genet A 2020; 182:2715-2721. [PMID: 32856782 DOI: 10.1002/ajmg.a.61817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/01/2020] [Accepted: 07/18/2020] [Indexed: 12/25/2022]
Abstract
Spondyloepiphyseal dysplasia type Stanescu (SED-S) is a very rare type II collagenopathy. We describe an 8-year-old boy who presented with short trunk, C2-C3 vertebral fusion, hand, foot, leg and thigh pain, stiffness and limited joint mobility, and waddling gait. Radiographs showed platyspondyly with anterior wedging and endplate irregularities, broad femoral necks, and large epiphyses and epiphyseal equivalents. Differential diagnosis included progressive pseudorheumatoid dysplasia and SED-S. A skeletal dysplasia custom-designed NGS panel was performed and the heterozygous pathogenic variant c.620G>A; p.(Gly207Glu) in COL2A1 was detected, establishing the diagnosis of SED-S. Vertebral fusions, observed in our patient, have not been previously described in this dysplasia. This variant has not been previously associated with SED-S, but was reported in two other families with spondyloepiphyseal dysplasia. Thus, this case expands the clinical and mutational spectrum of SED-S and demonstrates that SED-S significantly overlaps with other skeletal dysplasias.
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Affiliation(s)
- André M Travessa
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal.,Institute of Histology and Developmental Biology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Francisca Díaz-González
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain.,Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Teresa Mirco
- Department of Physical Therapy and Rehabilitation, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Filipa Oliveira-Ramos
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Manuel Parrón-Pajares
- Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain.,Department of Radiology, Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Karen E Heath
- Institute of Medical & Molecular Genetics (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autonóma de Madrid (UAM), and CIBERER, ISCIII, Madrid, Spain.,Skeletal Dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, UAM, Madrid, Spain
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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12
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Abdulhadi-Atwan M, Klopstock T, Sharaf M, Weinberg-Shukron A, Renbaum P, Levy-Lahad E, Zangen D. The novel R211Q POP1 homozygous mutation causes different pathogenesis and skeletal changes from those of previously reported POP1-associated anauxetic dysplasia. Am J Med Genet A 2020; 182:1268-1272. [PMID: 32134183 DOI: 10.1002/ajmg.a.61538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/24/2022]
Abstract
Processing of Precursor RNA 1 (POP1) is a core protein component shared by two essential closely related eukaryotic ribonucleoprotein complexes: RNase MRP (the mitochondrial RNA processing ribonuclease) and RNase P. Recently, five patients harboring mutations in POP1 have been reported with severe spondylo-epi-metaphyseal dysplasia and extremely short stature. We report a unique clinical phenotype resulting from the novel homozygous R211Q POP1 mutation in three patients from one family, presenting with severe short stature but only subtle skeletal dysplastic changes that are merely metaphyseal. The RNA moiety of the RNase-MRP complex quantified in RNA extracted from peripheral lymphocytes was dramatically reduced in affected patients indicating instability of the enzymatic complex. However, pre5.8s rRNA, a substrate of RNase-MRP complex, was not accumulated in patients' RNA unlike in the previously reported POP1 mutations; this may explain the uniquely mild phenotype in our cases, and questions the assumption that alteration in ribosomal biogenesis is the pathophysiological basis for skeletal disorders caused by POP1 mutations. Finally, POP1 mutations should be considered in familial cases with severe short stature even when skeletal dysplasia is not strongly evident.
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Affiliation(s)
- Maha Abdulhadi-Atwan
- Pediatric Endocrinology Service, Palestine Red Crescent Society Hospital, Hebron, Palestine
| | - Tehila Klopstock
- Medical Genetics Institute, Share Zedek Medical Center, Jerusalem, Israel.,The Hebrew University School of Medicine, Jerusalem, Israel
| | - Muna Sharaf
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariella Weinberg-Shukron
- Medical Genetics Institute, Share Zedek Medical Center, Jerusalem, Israel.,The Hebrew University School of Medicine, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Share Zedek Medical Center, Jerusalem, Israel
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Share Zedek Medical Center, Jerusalem, Israel.,The Hebrew University School of Medicine, Jerusalem, Israel
| | - David Zangen
- The Hebrew University School of Medicine, Jerusalem, Israel.,Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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13
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Díaz-González F, Parrón-Pajares M, Barcia-Ramirez A, Heath KE. First case of compound heterozygous BHLHA9 variants in mesoaxial synostotic syndactyly with phalangeal reduction. Am J Med Genet A 2020; 182:628-631. [PMID: 31912643 DOI: 10.1002/ajmg.a.61480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/22/2019] [Indexed: 12/23/2022]
Abstract
Mesoaxial synostotic syndactyly with phalangeal reduction (MSSD) is an extremely rare autosomal recessive limb abnormality characterized by the fusion of third and fourth fingers. To date, only homozygous missense and frameshift mutations have been reported in BHLHA9 associated to MSSD. In this study, we report a patient who presented with clinical and radiological features of MSSD. A customized skeletal dysplasia NGS panel revealed the presence of two novel compounds heterozygous variants in BHLHA9: NM_001164405.1: c.[226A>T][269G>C]; p.[(Lys76*)][(Arg90Pro)]. Thus, this is the first case of MSSD in a nonconsanguineous family.
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Affiliation(s)
- Francisca Díaz-González
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Manuel Parrón-Pajares
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Radiology, Hospital Universitario la Paz, Madrid, Spain
| | - Ana Barcia-Ramirez
- Department of Pediatrics, Hospital Universitario Virgen de Valme, Sevilla, Spain
| | - Karen E Heath
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U753), Instituto Carlos III, Madrid, Spain
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14
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An emerging ribosomopathy affecting the skeleton due to biallelic variations in NEPRO. Am J Med Genet A 2019; 179:1709-1717. [DOI: 10.1002/ajmg.a.61267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 01/02/2023]
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15
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Shastrula PK, Lund PJ, Garcia BA, Janicki SM. Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. J Biol Chem 2018; 293:12360-12377. [PMID: 29921582 DOI: 10.1074/jbc.ra118.001845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/30/2018] [Indexed: 01/26/2023] Open
Abstract
The histone H3 variant H3.3 is a highly conserved and dynamic regulator of chromatin organization. Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance. We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly. Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N terminus, and we identify a novel interaction with histone H2B at an adjacent site. The fact that archaeal Rpp29 does not include this N-terminal region suggests that it evolved to regulate eukaryote-specific functions. Oncogenic H3.3 mutations alter the H3.3-Rpp29 interaction, which suggests that they could dysregulate Rpp29 function in chromatin assembly. We also used KNS42 cells, an H3.3(G34V) pediatric high-grade glioma cell line, to show that Rpp29 1) represses H3.3 incorporation into transcriptionally active protein-coding, rRNA, and tRNA genes; 2) represses mRNA, protein expression, and antisense RNA; and 3) represses euchromatic post-translational modifications (PTMs) and promotes heterochromatic PTM deposition (i.e. histone H3 Lys-9 trimethylation (H3K9me3) and H3.1/2/3K27me3). Notably, we also found that K27me2 is increased and K36me1 decreased on H3.3(G34V), which suggests that Gly-34 mutations dysregulate Lys-27 and Lys-36 methylation in cis The fact that Rpp29 represses H3.3 chromatin assembly and sense and antisense RNA and promotes H3K9me3 and H3K27me3 suggests that Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites.
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Affiliation(s)
- Prashanth Krishna Shastrula
- From the Wistar Institute, Philadelphia, Pennsylvania 19104.,the Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, and
| | - Peder J Lund
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Susan M Janicki
- From the Wistar Institute, Philadelphia, Pennsylvania 19104,
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16
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Sentchordi-Montané L, Aza-Carmona M, Benito-Sanz S, Barreda-Bonis AC, Sánchez-Garre C, Prieto-Matos P, Ruiz-Ocaña P, Lechuga-Sancho A, Carcavilla-Urquí A, Mulero-Collantes I, Martos-Moreno GA, Del Pozo A, Vallespín E, Offiah A, Parrón-Pajares M, Dinis I, Sousa SB, Ros-Pérez P, González-Casado I, Heath KE. Heterozygous aggrecan variants are associated with short stature and brachydactyly: Description of 16 probands and a review of the literature. Clin Endocrinol (Oxf) 2018; 88:820-829. [PMID: 29464738 DOI: 10.1111/cen.13581] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Mutations in the aggrecan gene (ACAN) have been identified in two autosomal dominant skeletal dysplasias, spondyloepiphyseal dysplasia, Kimberley type (SEDK), and osteochondritis dissecans, as well as in a severe recessive dysplasia, spondyloepimetaphyseal dysplasia, aggrecan type. Next-generation sequencing (NGS) has aided the identification of heterozygous ACAN mutations in individuals with short stature, minor skeletal defects and mild facial dysmorphisms, some of whom have advanced bone age (BA), poor pubertal spurt and early growth cessation as well as precocious osteoarthritis. DESIGN AND METHODS This study involves clinical and genetic characterization of 16 probands with heterozygous ACAN variants, 14 with short stature and mild skeletal defects (group 1) and two with SEDK (group 2). Subsequently, we reviewed the literature to determine the frequency of the different clinical characteristics in ACAN-positive individuals. RESULTS A total of 16 ACAN variants were located throughout the gene, six pathogenic mutations and 10 variants of unknown significance (VUS). Interestingly, brachydactyly was observed in all probands. Probands from group 1 with a pathogenic mutation tended to be shorter, and 60% had an advanced BA compared to 0% in those with a VUS. A higher incidence of coxa valga was observed in individuals with a VUS (37% vs 0%). Nevertheless, other features were present at similar frequencies. CONCLUSIONS ACAN should be considered as a candidate gene in patients with short stature and minor skeletal defects, particularly those with brachydactyly, and in patients with spondyloepiphyseal dysplasia. It is also important to note that advanced BA and osteoarticular complications are not obligatory conditions for aggrecanopathies/aggrecan-associated dysplasias.
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Affiliation(s)
- Lucía Sentchordi-Montané
- Department of Pediatrics, Hospital Universitario Infanta Leonor, Madrid, Spain
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
| | - Miriam Aza-Carmona
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Sara Benito-Sanz
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Ana C Barreda-Bonis
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Pediatric Endocrinology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Pablo Prieto-Matos
- Department of Pediatrics, Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario Salamanca, Salamanca, Spain
| | - Pablo Ruiz-Ocaña
- Department of Pediatrics, Hospital Universitario Puerta del Mar, Cádiz, Spain
| | | | | | | | - Gabriel A Martos-Moreno
- Department of Endocrinology, Instituto de Investigación Sanitaria La Princesa, Hospital Infantil Universitario Niño Jesús, Universidad Autonóma de Madrid, Madrid, Spain
- Department of Pediatrics, Universidad Autónoma de Madrid and CIBEROBN, ISCIII, Madrid, Spain
| | - Angela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Elena Vallespín
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
| | - Amaka Offiah
- Department of Oncology and Metabolism, Academic Unit of Child Health, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Manuel Parrón-Pajares
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Pediatric Radiology, Hospital Universitario La Paz, Madrid, Spain
| | - Isabel Dinis
- Department of Pediatric Endocrinology, Diabetes and Growth Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar de Coimbra, Coimbra, Portugal
| | - Purificación Ros-Pérez
- Department of Pediatrics, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - Isabel González-Casado
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- Department of Pediatric Endocrinology, Hospital Universitario La Paz, Madrid, Spain
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autonóma de Madrid, IdiPAZ, Madrid, Spain
- Skeletal dysplasia Multidisciplinary Unit (UMDE), Hospital Universitario La Paz, Madrid, Spain
- CIBERER, ISCIII, Madrid, Spain
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