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Daly AF, Dunnington LA, Rodriguez-Buritica DF, Spiegel E, Brancati F, Mantovani G, Rawal VM, Faucz FR, Hijazi H, Caberg JH, Nardone AM, Bengala M, Fortugno P, Del Sindaco G, Ragonese M, Gould H, Cannavò S, Pétrossians P, Lania A, Lupski JR, Beckers A, Stratakis CA, Levy B, Trivellin G, Franke M. Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus. Genome Med 2024; 16:112. [PMID: 39272130 PMCID: PMC11396275 DOI: 10.1186/s13073-024-01378-5] [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: 05/16/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND X-linked acrogigantism (X-LAG; MIM: 300942) is a severe form of pituitary gigantism caused by chromosome Xq26.3 duplications involving GPR101. X-LAG-associated duplications disrupt the integrity of the topologically associating domain (TAD) containing GPR101 and lead to the formation of a neo-TAD that drives pituitary GPR101 misexpression and gigantism. As X-LAG is fully penetrant and heritable, duplications involving GPR101 identified on prenatal screening studies, like amniocentesis, can pose an interpretation challenge for medical geneticists and raise important concerns for patients and families. Therefore, providing robust information on the functional genomic impact of such duplications has important research and clinical value with respect to gene regulation and triplosensitivity traits. METHODS We employed 4C/HiC-seq as a clinical tool to determine the functional impact of incidentally discovered GPR101 duplications on TAD integrity in three families. After defining duplications and breakpoints around GPR101 by clinical-grade and high-density aCGH, we constructed 4C/HiC chromatin contact maps for our study population and compared them with normal and active (X-LAG) controls. RESULTS We showed that duplications involving GPR101 that preserved the centromeric invariant TAD boundary did not generate a pathogenic neo-TAD and that ectopic enhancers were not adopted. This allowed us to discount presumptive/suspected X-LAG diagnoses and GPR101 misexpression, obviating the need for intensive clinical follow-up. CONCLUSIONS This study highlights the importance of TAD boundaries and chromatin interactions in determining the functional impact of copy number variants and provides proof-of-concept for using 4C/HiC-seq as a clinical tool to acquire crucial information for genetic counseling and to support clinical decision-making in cases of suspected TADopathies.
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Affiliation(s)
- Adrian F Daly
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Liège, Belgium
| | - Leslie A Dunnington
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center (UTHealth Houston), Houston, TX, USA
- Memorial Hermann-Texas Medical Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David F Rodriguez-Buritica
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center (UTHealth Houston), Houston, TX, USA
- Memorial Hermann-Texas Medical Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Erica Spiegel
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Francesco Brancati
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Spennati N.1, L'Aquila, 67010, Italy
- Human Functional Genetics Laboratory, IRCCS San Raffaele Roma, Rome, Italy
| | - Giovanna Mantovani
- Endocrinology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Vandana M Rawal
- Austin Diagnostic Clinic, 2400 Cedar Bend Dr, Austin, TX, 78758, USA
| | - Fabio Rueda Faucz
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jean-Hubert Caberg
- Department of Human Genetics, Centre Hospitalier Universitaire de Liège, University of Liège, Liège, Belgium
| | - Anna Maria Nardone
- Medical Genetics Laboratory, Policlinico Tor Vergata Hospital, Viale Oxford 81, Rome, 00133, Italy
| | - Mario Bengala
- Medical Genetics Laboratory, Policlinico Tor Vergata Hospital, Viale Oxford 81, Rome, 00133, Italy
| | - Paola Fortugno
- Human Functional Genetics Laboratory, IRCCS San Raffaele Roma, Rome, Italy
- Università Telematica San Raffaele, Rome, Italy
| | - Giulia Del Sindaco
- Endocrinology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Marta Ragonese
- Department of Human Pathology of Adulthood and Childhood DETEV, Endocrinology Unit, University of Messina, 98125, Messina, Italy
| | - Helen Gould
- Austin Maternal Fetal Medicine, 12200 Renfert Way Ste G3, Austin, TX, 78758, USA
| | - Salvatore Cannavò
- Department of Human Pathology of Adulthood and Childhood DETEV, Endocrinology Unit, University of Messina, 98125, Messina, Italy
| | - Patrick Pétrossians
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Liège, Belgium
| | - Andrea Lania
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, Milan, 20072, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Albert Beckers
- Department of Endocrinology, Centre Hospitalier Universitaire de Liège, University of Liège, Liège, Belgium
| | - Constantine A Stratakis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
- Human Genetics and Precision Medicine, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas, Heraklion, Greece
- ASTREA Health, Athens, Greece
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, Milan, 20072, Italy.
- IRCCS Humanitas Research Hospital, Milan, Italy.
| | - Martin Franke
- Andalusian Center for Developmental Biology (CABD), Junta de Andalucia - Universidad Pablo de Olavide (UPO) - Consejo Superior de Investigaciones Cientificas (CSIC), Seville, Spain.
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Rufibach L, Berger K, Chakravorty S, Emmons S, Long L, Gibson G, Hegde M. Utilization of Targeted RNA-Seq for the Resolution of Variant Pathogenicity and Enhancement of Diagnostic Yield in Dysferlinopathy. J Pers Med 2023; 13:jpm13030520. [PMID: 36983702 PMCID: PMC10056012 DOI: 10.3390/jpm13030520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
For inherited diseases, obtaining a definitive diagnosis is critical for proper disease management, family planning, and participation in clinical trials. This can be challenging for dysferlinopathy due to the significant clinical overlap between the 30+ subtypes of limb–girdle muscular dystrophy (LGMD) and the large number of variants of unknown significance (VUSs) that are identified in the dysferlin gene, DYSF. We performed targeted RNA-Seq using a custom gene-panel in 77 individuals with a clinical/genetic suspicion of dysferlinopathy and evaluated all 111 identified DYSF variants according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. This evaluation identified 11 novel DYSF variants and allowed for the classification of 87 DYSF variants as pathogenic/likely pathogenic, 8 likely benign, while 16 variants remained VUSs. By the end of the study, 60 of the 77 cases had a definitive diagnosis of dysferlinopathy, which was a 47% increase in diagnostic yield over the rate at study onset. This data shows the ability of RNA-Seq to assist in variant pathogenicity classification and diagnosis of dysferlinopathy and is, therefore, a type of analysis that should be considered when DNA-based genetic analysis is not sufficient to provide a definitive diagnosis.
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Affiliation(s)
- Laura Rufibach
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
- Correspondence:
| | - Kiera Berger
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA; (K.B.); (G.G.)
| | - Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.C.); (M.H.)
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sarah Emmons
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
| | - Laurie Long
- Jain Foundation, Inc., Seattle, WA 98115, USA; (S.E.); (L.L.)
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA; (K.B.); (G.G.)
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; (S.C.); (M.H.)
- PerkinElmer Genomics, Global Laboratory Services, Waltham, MA 02451, USA
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Morales R, Lledo B, Ortiz JA, Lozano FM, Garcia EM, Bernabeu A, Fuentes A, Bernabeu R. Identification of new variants and candidate genes in women with familial premature ovarian insufficiency using whole-exome sequencing. J Assist Reprod Genet 2022; 39:2595-2605. [PMID: 36208357 PMCID: PMC9723088 DOI: 10.1007/s10815-022-02629-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/24/2022] [Indexed: 11/30/2022] Open
Abstract
PURPOSE To identify candidate variants in genes possibly associated with premature ovarian insufficiency (POI). METHODS Fourteen women, from 7 families, affected by idiopathic POI were included. Additionally, 98 oocyte donors of the same ethnicity were enrolled as a control group. Whole-exome sequencing (WES) was performed in 14 women with POI to identify possibly pathogenic variants in genes potentially associated with the ovarian function. The candidate genes selected in POI patients were analysed within the exome results of oocyte donors. RESULTS After the variant filtering in the WES analysis of 7 POI families, 23 possibly damaging genetic variants were identified in 22 genes related to POI or linked to ovarian physiology. All variants were heterozygous and five of the seven families carried two or more variants in different genes. We have described genes that have never been associated to POI pathology; however, they are involved in important biological processes for ovarian function. In the 98 oocyte donors of the control group, we found no potentially pathogenic variants among the 22 candidate genes. CONCLUSION WES has previously shown as an efficient tool to identify causative genes for ovarian failure. Although some studies have focused on it, and many genes are identified, this study proposes new candidate genes and variants, having potentially moderate/strong functional effects, associated with POI, and argues for a polygenic etiology of POI in some cases.
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Affiliation(s)
- R Morales
- Molecular Biology, Instituto Bernabeu, 03016, Alicante, Spain.
| | - B Lledo
- Molecular Biology, Instituto Bernabeu, 03016, Alicante, Spain
| | - J A Ortiz
- Molecular Biology, Instituto Bernabeu, 03016, Alicante, Spain
| | - F M Lozano
- Molecular Biology, Instituto Bernabeu, 03016, Alicante, Spain
| | - E M Garcia
- Molecular Biology, Instituto Bernabeu, 03016, Alicante, Spain
| | - A Bernabeu
- Reproductive Medicine, Instituto Bernabeu, 03016, Alicante, Spain
| | - A Fuentes
- Reproductive Medicine, Instituto Bernabeu, 03016, Alicante, Spain
| | - R Bernabeu
- Reproductive Medicine, Instituto Bernabeu, 03016, Alicante, Spain
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Yang Y, Glidden MD, Dhayalan B, Zaykov AN, Chen YS, Wickramasinghe NP, DiMarchi RD, Weiss MA. Peptide Model of the Mutant Proinsulin Syndrome. II. Nascent Structure and Biological Implications. Front Endocrinol (Lausanne) 2022; 13:821091. [PMID: 35299958 PMCID: PMC8922542 DOI: 10.3389/fendo.2022.821091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Toxic misfolding of proinsulin variants in β-cells defines a monogenic diabetes syndrome, designated mutant INS-gene induced diabetes of the young (MIDY). In our first study (previous article in this issue), we described a one-disulfide peptide model of a proinsulin folding intermediate and its use to study such variants. The mutations (LeuB15→Pro, LeuA16→Pro, and PheB24→Ser) probe residues conserved among vertebrate insulins. In this companion study, we describe 1H and 1H-13C NMR studies of the peptides; key NMR resonance assignments were verified by synthetic 13C-labeling. Parent spectra retain nativelike features in the neighborhood of the single disulfide bridge (cystine B19-A20), including secondary NMR chemical shifts and nonlocal nuclear Overhauser effects. This partial fold engages wild-type side chains LeuB15, LeuA16 and PheB24 at the nexus of nativelike α-helices α1 and α3 (as defined in native proinsulin) and flanking β-strand (residues B24-B26). The variant peptides exhibit successive structural perturbations in order: parent (most organized) > SerB24 >> ProA16 > ProB15 (least organized). The same order pertains to (a) overall α-helix content as probed by circular dichroism, (b) synthetic yields of corresponding three-disulfide insulin analogs, and (c) ER stress induced in cell culture by corresponding mutant proinsulins. These findings suggest that this and related peptide models will provide a general platform for classification of MIDY mutations based on molecular mechanisms by which nascent disulfide pairing is impaired. We propose that the syndrome's variable phenotypic spectrum-onsets ranging from the neonatal period to later in childhood or adolescence-reflects structural features of respective folding intermediates.
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Affiliation(s)
- Yanwu Yang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michael D. Glidden
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Balamurugan Dhayalan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Yen-Shan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Nalinda P. Wickramasinghe
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | | | - Michael A. Weiss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
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Martínez Quiñones JV, Aso Escario J, Sebastián Sebastián C, Bares Fernández I, Consolini Rossi F, Arregui Calvo R. Spinal health in 40 patients in the initial stage of laboural life. Morfogeometric, biological and environmental study. Orthop Rev (Pavia) 2022; 14:30169. [PMID: 35106128 DOI: 10.52965/001c.30169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 11/06/2022] Open
Abstract
Introduction Assuming that spinal shape is a genetic expression, its analysis and acquired factors could assess their respective contribution to early spine deterioration. Material and methods A geometric morphometric analysis was retrospectively performed on sagittal lumbar MRI of young patients with back pain to identify lumbar spine shape changes. Using Geometric Morphometrics, findings were analyzed with anthropometric, radiological, and clinical variables. Results 80 cases under 26 years of age were collected, 55 men (mean age 22.81) and 25 women (mean age 23.24). MRI abnormalities were reported in 57.5%: single altered disc (N=17), root compromises (N=8), and transition anomalies (35%).In the non-normal MRI subgroup, shape variation included: increased lordosis, enlarged vertebral body, canal stenosis, and lumbarization of S1. In non-Spanish origin patients, lumbar straightening and segmental deformities were prevalent. Morphometrics findings showed that lumbosacral transition anomalies are frequently underreported. Conclusions Genetic factors could be the main determinants of abnormality in MRIs under 26 years. The primary markers are transitional abnormalities, segmental deformities, and canal stenosis. In foreign populations, shape changes could suggest spine overload at an early age.
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Basel-Salmon L, Sukenik-Halevy R. Challenges in variant interpretation in prenatal exome sequencing. Eur J Med Genet 2021; 65:104410. [PMID: 34952236 DOI: 10.1016/j.ejmg.2021.104410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/05/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
The use of exome sequencing (ES) in the prenatal setting improves the diagnostic yield of genetic testing for fetuses with ultrasound anomalies. However, while the purpose of ES is to explain the fetal phenotype, secondary or incidental findings unrelated to the observed abnormalities might be detected. Recently, requests for ES in fetuses with no sonographic abnormalities have been increasing, raising serious ethical and medico-legal concerns. Variant interpretation is complex even in the postnatal setting and performing broad genomic data analyses in the prenatal setting presents additional dilemmas. This article discusses challenges and questions related to prenatal ES, including variant interpretation of incidental findings in cases of indicated prenatal ES, as well as in situations where ES is performed in asymptomatic fetuses.
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Affiliation(s)
- Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Hospital, Petach Tikva, Israel; Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel.
| | - Rivka Sukenik-Halevy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Genetics Institute, Meir Medical Center, Kfar Saba, Israel
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Tangaro MA, Mandreoli P, Chiara M, Donvito G, Antonacci M, Parisi A, Bianco A, Romano A, Bianchi DM, Cangelosi D, Uva P, Molineris I, Nosi V, Calogero RA, Alessandri L, Pedrini E, Mordenti M, Bonetti E, Sangiorgi L, Pesole G, Zambelli F. Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinformatics 2021; 22:544. [PMID: 34749633 PMCID: PMC8574934 DOI: 10.1186/s12859-021-04401-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of "on-demand" Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server's initial configuration and deployment. RESULTS "Laniakea@ReCaS", the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. CONCLUSIONS During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers' work.
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Affiliation(s)
- Marco Antonio Tangaro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Pietro Mandreoli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy
| | - Matteo Chiara
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy
| | - Giacinto Donvito
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Marica Antonacci
- National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Angelo Romano
- National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy
| | - Davide Cangelosi
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Paolo Uva
- Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
- Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy
| | - Ivan Molineris
- Department of Life Science and System Biology, University of Turin, Via Accademia Albertina, 13-1023, Turin, Italy
| | - Vladimir Nosi
- Department of Computer Science, University of Turin, Via Pessinetto 12, 10049, Turin, Italy
| | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy
| | - Luca Alessandri
- Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy
| | - Elena Pedrini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Emanuele Bonetti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126, Bari, Italy.
| | - Federico Zambelli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy.
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Kato H, Shimizu M, Urano T. Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos. BMC Bioinformatics 2021; 22:322. [PMID: 34120589 PMCID: PMC8201924 DOI: 10.1186/s12859-021-04240-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Assessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods for predicting nucleosome positioning include bioinformatics and biophysical approaches. An advantage of bioinformatics methods, which are based on in vivo nucleosome maps, is the use of natural sequences that may contain previously unknown elements involved in nucleosome positioning in vivo. The accuracy of such prediction attempts reflects the genomic coordinate resolution of the nucleosome maps applied. Nucleosome maps are constructed using micrococcal nuclease digestion followed by high-throughput sequencing (MNase-seq). However, as MNase has a strong preference for A/T-rich sequences, MNase-seq may not be appropriate for this purpose. In addition to MNase-seq-based maps, base pair-resolution chemical maps of in vivo nucleosomes from three different species (budding and fission yeasts, and mice) are currently available. However, these chemical maps have yet to be integrated into publicly available computational methods. Results We developed a Bioconductor package (named nuCpos) to demonstrate the superiority of chemical maps in predicting nucleosome positioning. The accuracy of chemical map-based prediction in rotational settings was higher than that of the previously developed MNase-seq-based approach. With our method, predicted nucleosome occupancy reasonably matched in vivo observations and was not affected by A/T nucleotide frequency. Effects of genetic alterations on nucleosome positioning that had been observed in living yeast cells could also be predicted. nuCpos calculates individual histone binding affinity (HBA) scores for given 147-bp sequences to examine their suitability for nucleosome formation. We also established local HBA as a new parameter to predict nucleosome formation, which was calculated for 13 overlapping nucleosomal DNA subsequences. HBA and local HBA scores for various sequences agreed well with previous in vitro and in vivo studies. Furthermore, our results suggest that nucleosomal subsegments that are disfavored in different rotational settings contribute to the defined positioning of nucleosomes. Conclusions Our results demonstrate that chemical map-based statistical models are beneficial for studying nucleosomal DNA features. Studies employing nuCpos software can enhance understanding of chromatin regulation and the interpretation of genetic alterations and facilitate the design of artificial sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04240-2.
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Affiliation(s)
- Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan.
| | - Mitsuhiro Shimizu
- Department of Chemistry, Graduate School of Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo, 191-8506, Japan
| | - Takeshi Urano
- Department of Biochemistry, Shimane University School of Medicine, 89-1 Enya-cho, Izumo, Shimane, 693-8501, Japan
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10
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Yamashita M, Inoue K, Okano T, Morio T. Inborn errors of immunity-recent advances in research on the pathogenesis. Inflamm Regen 2021; 41:9. [PMID: 33766139 PMCID: PMC7992775 DOI: 10.1186/s41232-021-00159-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 11/15/2022] Open
Abstract
Primary immunodeficiency (PID) is a genetic disorder with a defect of one of the important components of our immune system. Classical PID has been recognized as a disorder with loss of function of the immune system. Recent studies have unveiled disorders with immune dysfunction with autoimmunity, autoinflammation, allergy, or predisposition to malignancy. Some of them were caused by an augmented immune function or a defect in immune regulation. With this background, the term inborn errors of immunity (IEI) is now used to refer to PID in the International Union of Immunological Societies (IUIS) classification. More than 400 responsible genes have been identified in patients with IEI so far, and importantly, many of them identified lately were caused by a heterologous mutation. Moreover, the onset is not necessarily in childhood, and we started seeing more and more IEI patients diagnosed in adulthood in the clinical settings. Recent advances in genetic analysis, including whole-exome analysis, whole-genome analysis, and RNA-seq have contributed to the identification of the disease-causing gene mutation. We also started to find heterogeneity of phenotype even in the patients with the same mutation in the same family, leading us to wonder if modifier gene or epigenetic modification is involved in the pathogenesis. In contrast, we accumulated many cases suggesting genetic heterogeneity is associated with phenotypic homogeneity. It has thus become difficult to deduce a responsible gene only from the phenotype in a certain type of IEI. Current curative therapy for IEI includes hematopoietic cell transplantation and gene therapy. Other curative therapeutic modalities have been long waited and are to be introduced in the future. These include a small molecule that inhibits the gain-of-function of the molecule- and genome-editing technology. Research on IEI will surely lead to a better understanding of other immune-related disorders including rheumatic diseases and atopic disorders.
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Affiliation(s)
- Motoi Yamashita
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kento Inoue
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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11
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Chakravorty S, Nallamilli BRR, Khadilkar SV, Singla MB, Bhutada A, Dastur R, Gaitonde PS, Rufibach LE, Gloster L, Hegde M. Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent. Front Neurol 2020; 11:559327. [PMID: 33250842 PMCID: PMC7674836 DOI: 10.3389/fneur.2020.559327] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Inherited myopathies comprise more than 200 different individually rare disease-subtypes, but when combined together they have a high prevalence of 1 in 6,000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods: In this cohort study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results: Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42–56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy), and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. Seventy-eight percent of the DYSF patients were homozygous for the detected pathogenic variant, suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). Thirteen patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity/digenic-contribution to disease presentation and progression. Conclusions: Application of clinically correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically driven molecular diagnostics.
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Affiliation(s)
- Samya Chakravorty
- Emory University Department of Pediatrics, Atlanta, GA, United States.,Emory University Department of Human Genetics, Atlanta, GA, United States.,Division of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Satish Vasant Khadilkar
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | - Madhu Bala Singla
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | | | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | - Pradnya Satish Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | | | - Logan Gloster
- Emory University Department of Pediatrics, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Madhuri Hegde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PerkinElmer Genomics, Global Laboratory Services, Waltham, MA, United States
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12
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Anderson CD. Exome Sequencing in Suspected Monogenic Stroke. Stroke 2020; 51:1047-1048. [DOI: 10.1161/strokeaha.120.028817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Christopher D. Anderson
- From the Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston; McCance Center for Brain Health, Massachusetts General Hospital, Boston; and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
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13
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Salinas-Torres VM, Gallardo-Blanco HL, Salinas-Torres RA, Cerda-Flores RM, Lugo-Trampe JJ, Villarreal-Martínez DZ, Ibarra-Ramírez M, Martínez de Villarreal LE. Whole exome sequencing identifies multiple novel candidate genes in familial gastroschisis. Mol Genet Genomic Med 2020; 8:e1176. [PMID: 32163230 PMCID: PMC7216806 DOI: 10.1002/mgg3.1176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 01/18/2020] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Background Genetic association studies for gastroschisis have highlighted several candidate variants. However, genetic basis in gastroschisis from noninvestigated heritable factors could provide new insights into the human biology for this birth defect. We aim to identify novel gastroschisis susceptibility variants by employing whole exome sequencing (WES) in a Mexican family with recurrence of gastroschisis. Methods We employed WES in two affected half‐sisters with gastroschisis, mother, and father of the proband. Additionally, functional bioinformatics analysis was based on SVS–PhoRank and Ensembl–Variant Effect Predictor. The latter assessed the potentially deleterious effects (high, moderate, low, or modifier impact) from exome variants based on SIFT, PolyPhen, dbNSFP, Condel, LoFtool, MaxEntScan, and BLOSUM62 algorithms. The analysis was based on the Human Genome annotation, GRCh37/hg19. Candidate genes were prioritized and manually curated based on significant phenotypic relevance (SVS–PhoRank) and functional properties (Ensembl–Variant Effect Predictor). Functional enrichment analysis was performed using ToppGene Suite, including a manual curation of significant Gene Ontology (GO) biological processes from functional similarity analysis of candidate genes. Results No single gene‐disrupting variant was identified. Instead, 428 heterozygous variations were identified for which SPATA17, PDE4DIP, CFAP65, ALPP, ZNF717, OR4C3, MAP2K3, TLR8, and UBE2NL were predicted as high impact in both cases, mother, and father of the proband. PLOD1, COL6A3, FGFRL1, HHIP, SGCD, RAPGEF1, PKD1, ZFHX3, BCAS3, EVPL, CEACAM5, and KLK14 were segregated among both cases and mother. Multiple interacting background modifiers may regulate gastroschisis susceptibility. These candidate genes highlight a role for development of blood vessel, circulatory system, muscle structure, epithelium, and epidermis, regulation of cell junction assembly, biological/cell adhesion, detection/response to endogenous stimulus, regulation of cytokine biosynthetic process, response to growth factor, postreplication repair/protein K63‐linked ubiquitination, protein‐containing complex assembly, and regulation of transcription DNA‐templated. Conclusion Considering the likely gene‐disrupting prediction results and similar biological pattern of mechanisms, we propose a joint “multifactorial model” in gastroschisis pathogenesis.
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Affiliation(s)
- Víctor M Salinas-Torres
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Hugo L Gallardo-Blanco
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | | | | | - José J Lugo-Trampe
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Daniel Z Villarreal-Martínez
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Marisol Ibarra-Ramírez
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
| | - Laura E Martínez de Villarreal
- Department of Genetics, School of Medicine and University Hospital Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, México
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14
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Elbracht M, Meyer R, Eggermann T, Kurth I. [Rational use of genetic tests in internal medicine : Possibilities and limitations of next generation sequencing diagnostics]. Internist (Berl) 2019; 59:756-765. [PMID: 29946883 DOI: 10.1007/s00108-018-0457-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND New methods of molecular genetic diagnostics enable a more comprehensive genetic analysis of patients. OBJECTIVES Rational use and benefits of molecular genetic testing in patients with various internal diseases. METHOD Evaluation of topic-related literature, discussion of own experiences, as well as consideration of current guidelines. RESULTS New genetic tests, such as next generation sequencing (NGS), improve the diagnosis of hereditary diseases; however, the use of this technology also leads to additional findings, which must be carefully considered. CONCLUSION The rational use of genetic tests is a benefit for patients and can significantly influence the prevention and treatment of a disease. The increasing complexity of genetic findings requires interdisciplinary approaches involving human genetics, internal medicine, and other disciplines.
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Affiliation(s)
- M Elbracht
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - R Meyer
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - T Eggermann
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - I Kurth
- Institut für Humangenetik, Uniklinik RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland.
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15
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Exome sequencing and bioinformatic approaches reveals rare sequence variants involved in cell signalling and elastic fibre homeostasis: new evidence in the development of ectopic calcification. Cell Signal 2019; 59:131-140. [DOI: 10.1016/j.cellsig.2019.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022]
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16
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Beaver SK, Mesa-Torres N, Pey AL, Timson DJ. NQO1: A target for the treatment of cancer and neurological diseases, and a model to understand loss of function disease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:663-676. [PMID: 31091472 DOI: 10.1016/j.bbapap.2019.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
NAD(P)H quinone oxidoreductase 1 (NQO1) is a multi-functional protein that catalyses the reduction of quinones (and other molecules), thus playing roles in xenobiotic detoxification and redox balance, and also has roles in stabilising apoptosis regulators such as p53. The structure and enzymology of NQO1 is well-characterised, showing a substituted enzyme mechanism in which NAD(P)H binds first and reduces an FAD cofactor in the active site, assisted by a charge relay system involving Tyr-155 and His-161. Protein dynamics play important role in physio-pathological aspects of this protein. NQO1 is a good target to treat cancer due to its overexpression in cancer cells. A polymorphic form of NQO1 (p.P187S) is associated with increased cancer risk and certain neurological disorders (such as multiple sclerosis and Alzheimer´s disease), possibly due to its roles in the antioxidant defence. p.P187S has greatly reduced FAD affinity and stability, due to destabilization of the flavin binding site and the C-terminal domain, which leading to reduced activity and enhanced degradation. Suppressor mutations partially restore the activity of p.P187S by local stabilization of these regions, and showing long-range allosteric communication within the protein. Consequently, the correction of NQO1 misfolding by pharmacological chaperones is a viable strategy, which may be useful to treat cancer and some neurological conditions, targeting structural spots linked to specific disease-mechanisms. Thus, NQO1 emerges as a good model to investigate loss of function mechanisms in genetic diseases as well as to improve strategies to discriminate between neutral and pathogenic variants in genome-wide sequencing studies.
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Affiliation(s)
- Sarah K Beaver
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain
| | - Angel L Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071, Spain.
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
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17
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Bioinformatic Analysis of Gene Variants from Gastroschisis Recurrence Identifies Multiple Novel Pathogenetic Pathways: Implication for the Closure of the Ventral Body Wall. Int J Mol Sci 2019; 20:ijms20092295. [PMID: 31075877 PMCID: PMC6539040 DOI: 10.3390/ijms20092295] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
We investigated whether likely pathogenic variants co-segregating with gastroschisis through a family-based approach using bioinformatic analyses were implicated in body wall closure. Gene Ontology (GO)/Panther functional enrichment and protein-protein interaction analysis by String identified several biological networks of highly connected genes in UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9, UGT1A10, AOX1, NOTCH1, HIST1H2BB, RPS3, THBS1, ADCY9, and FGFR4. SVS–PhoRank identified a dominant model in OR10G4 (also as heterozygous de novo), ITIH3, PLEKHG4B, SLC9A3, ITGA2, AOX1, and ALPP, including a recessive model in UGT1A7, UGT1A6, PER2, PTPRD, and UGT1A3. A heterozygous compound model was observed in CDYL, KDM5A, RASGRP1, MYBPC2, PDE4DIP, F5, OBSCN, and UGT1A. These genes were implicated in pathogenetic pathways involving the following GO related categories: xenobiotic, regulation of metabolic process, regulation of cell adhesion, regulation of gene expression, inflammatory response, regulation of vascular development, keratinization, left-right symmetry, epigenetic, ubiquitination, and regulation of protein synthesis. Multiple background modifiers interacting with disease-relevant pathways may regulate gastroschisis susceptibility. Based in our findings and considering the plausibility of the biological pattern of mechanisms and gene network modeling, we suggest that the gastroschisis developmental process may be the consequence of several well-orchestrated biological and molecular mechanisms which could be interacting with gastroschisis predispositions within the first ten weeks of development.
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18
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Nallamilli BRR, Chakravorty S, Kesari A, Tanner A, Ankala A, Schneider T, da Silva C, Beadling R, Alexander JJ, Askree SH, Whitt Z, Bean L, Collins C, Khadilkar S, Gaitonde P, Dastur R, Wicklund M, Mozaffar T, Harms M, Rufibach L, Mittal P, Hegde M. Genetic landscape and novel disease mechanisms from a large LGMD cohort of 4656 patients. Ann Clin Transl Neurol 2018; 5:1574-1587. [PMID: 30564623 PMCID: PMC6292381 DOI: 10.1002/acn3.649] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022] Open
Abstract
Objective Limb‐girdle muscular dystrophies (LGMDs), one of the most heterogeneous neuromuscular disorders (NMDs), involves predominantly proximal‐muscle weakness with >30 genes associated with different subtypes. The clinical‐genetic overlap among subtypes and with other NMDs complicate disease‐subtype identification lengthening diagnostic process, increases overall costs hindering treatment/clinical‐trial recruitment. Currently seven LGMD clinical trials are active but still no gene‐therapy‐related treatment is available. Till‐date no nation‐wide large‐scale LGMD sequencing program was performed. Our objectives were to understand LGMD genetic basis, different subtypes’ relative prevalence across US and investigate underlying disease mechanisms. Methods A total of 4656 patients with clinically suspected‐LGMD across US were recruited to conduct next‐generation sequencing (NGS)‐based gene‐panel testing during June‐2015 to June‐2017 in CLIA‐CAP‐certified Emory‐Genetics‐Laboratory. Thirty‐five LGMD‐subtypes‐associated or LGMD‐like other NMD‐associated genes were investigated. Main outcomes were diagnostic yield, gene‐variant spectrum, and LGMD subtypes’ prevalence in a large US LGMD‐suspected population. Results Molecular diagnosis was established in 27% (1259 cases; 95% CI, 26–29%) of the patients with major contributing genes to LGMD phenotypes being: CAPN3(17%), DYSF(16%), FKRP(9%) and ANO5(7%). We observed an increased prevalence of genetically confirmed late‐onset Pompe disease, DNAJB6‐associated LGMD subtype1E and CAPN3‐associated autosomal‐dominant LGMDs. Interestingly, we identified a high prevalence of patients with pathogenic variants in more than one LGMD gene suggesting possible synergistic heterozygosity/digenic/multigenic contribution to disease presentation/progression that needs consideration as a part of diagnostic modality. Interpretation Overall, this study has improved our understanding of the relative prevalence of different LGMD subtypes, their respective genetic etiology, and the changing paradigm of their inheritance modes and novel mechanisms that will allow for improved timely treatment, management, and enrolment of molecularly diagnosed individuals in clinical trials.
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Affiliation(s)
| | | | - Akanchha Kesari
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | - Alice Tanner
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | - Arunkanth Ankala
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | | | | | | | - John J Alexander
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | - Syed Hussain Askree
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | - Zachary Whitt
- Emory University Department of Human Genetics Atlanta Georgia 30322.,Augusta University Augusta Georgia 30912
| | - Lora Bean
- Emory University Department of Human Genetics Atlanta Georgia 30322.,EGL Genetics-Eurofins Tucker Atlanta Georgia 30084
| | - Christin Collins
- Emory University Department of Human Genetics Atlanta Georgia 30322
| | - Satish Khadilkar
- Department of Neurology Bombay Hospital Mumbai Maharashtra India.,Department of Neurology Sir J J Group of Hospitals Grant Medical College Mumbai Maharashtra India
| | - Pradnya Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND) 400022 Mumbai India
| | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND) 400022 Mumbai India
| | - Matthew Wicklund
- Neurology The University of Colorado at Denver - Anschutz Medical Campus Aurora Colorado 80045
| | - Tahseen Mozaffar
- Neurology University of California, Irvine Orange California 92868
| | - Matthew Harms
- Department of Neurology Columbia University New York New York 10032
| | | | | | - Madhuri Hegde
- Emory University Department of Human Genetics Atlanta Georgia 30322
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19
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Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
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Fichna JP, Maruszak A, Żekanowski C. Myofibrillar myopathy in the genomic context. J Appl Genet 2018; 59:431-439. [PMID: 30203143 DOI: 10.1007/s13353-018-0463-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/30/2018] [Indexed: 12/31/2022]
Abstract
Myofibrillar myopathy (MFM) is a group of inherited muscular disorders characterized by myofibril dissolution and abnormal accumulation of degradation products. The diagnosis of muscular disorders based on clinical presentation is difficult due to phenotypic heterogeneity and overlapping symptoms. In addition, precise diagnosis does not always explain the disease etiopathology or the highly variable clinical course even among patients diagnosed with the same type of myopathy. The advent of high-throughput next-generation sequencing (NGS) has provided a successful and cost-effective strategy for identification of novel causative genes in myopathies, including MFM. So far, pathogenic mutations associated with MFM phenotype, including atypical MFM-like cases, have been identified in 17 genes: DES, CRYAB, MYOT, ZASP, FLNC, BAG3, FHL1, TTN, DNAJB6, PLEC, LMNA, ACTA1, HSPB8, KY, PYROXD1, and SQSTM + TIA1 (digenic). Most of these genes are also associated with other forms of muscle diseases. In addition, in many MFM patients, numerous genomic variants in muscle-related genes have been identified. The various myopathies and muscular dystrophies seem to form a single disease continuum; therefore, gene identification in one disease impacts the genetic etiology of the others. In this review, we describe the heterogeneity of the MFM genetic background focusing on the role of rare variants, the importance of whole genome sequencing in the identification of novel disease-associated mutations, and the emerging concept of variant load as the basis of the phenotypic heterogeneity.
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Affiliation(s)
- Jakub Piotr Fichna
- Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106, Warsaw, Poland.
| | - Aleksandra Maruszak
- Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106, Warsaw, Poland
| | - Cezary Żekanowski
- Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106, Warsaw, Poland
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