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da Silva Franco JF, Neves RL, Menezes AN, Nogueira BR, Gomes CP, Pesquero JB. Hidden Aberrant Transcripts in TTC37 Cause Trichohepatoenteric Syndrome. Clin Genet 2024. [PMID: 39390792 DOI: 10.1111/cge.14630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/19/2024] [Accepted: 09/29/2024] [Indexed: 10/12/2024]
Abstract
The patient had clinical suspicion of THES. Complex genetic analyzes using WES, WGS were performed without success in the diagnosis. Further molecular analyzes using RNA and protein was necessary to reach the final correct THES diagnosis.
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2
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Ouahed JD, Griffith A, Collen LV, Snapper SB. Breaking Down Barriers: Epithelial Contributors to Monogenic IBD Pathogenesis. Inflamm Bowel Dis 2024; 30:1189-1206. [PMID: 38280053 DOI: 10.1093/ibd/izad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Indexed: 01/29/2024]
Abstract
Monogenic causes of inflammatory bowel diseases (IBD) are increasingly being discovered. To date, much attention has been placed in those resulting from inborn errors of immunity. Therapeutic efforts have been largely focused on offering personalized immune modulation or curative bone marrow transplant for patients with IBD and underlying immune disorders. To date, less emphasis has been placed on monogenic causes of IBD that pertain to impairment of the intestinal epithelial barrier. Here, we provide a comprehensive review of monogenic causes of IBD that result in impaired intestinal epithelial barrier that are categorized into 6 important functions: (1) epithelial cell organization, (2) epithelial cell intrinsic functions, (3) epithelial cell apoptosis and necroptosis, (4) complement activation, (5) epithelial cell signaling, and (6) control of RNA degradation products. We illustrate how impairment of any of these categories can result in IBD. This work reviews the current understanding of the genes involved in maintaining the intestinal barrier, the inheritance patterns that result in dysfunction, features of IBD resulting from these disorders, and pertinent translational work in this field.
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Affiliation(s)
- Jodie D Ouahed
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexandra Griffith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren V Collen
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
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3
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Avitzur Y, Jimenez L, Martincevic I, Acra S, Courtney-Martin G, Gray M, Hope K, Muise A, Prieto Jimenez PM, Taylor N, Thiagarajah JR, Martín MG. Diet management in congenital diarrheas and enteropathies - general concepts and disease-specific approach, a narrative review. Am J Clin Nutr 2024; 120:17-33. [PMID: 38734141 PMCID: PMC11251218 DOI: 10.1016/j.ajcnut.2024.05.004] [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: 11/07/2023] [Revised: 04/27/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
Congenital diarrheas and enteropathies (CODE) are a group of rare, heterogenous, monogenic disorders that lead to chronic diarrhea in infancy. Definitive treatment is rarely available, and supportive treatment is the mainstay. Nutritional management in the form of either specialized formulas, restrictive diet, or parenteral nutrition support in CODE with poor enteral tolerance is the cornerstone of CODE treatment and long-term growth. The evidence to support the use of specific diet regimens and nutritional approaches in most CODE disorders is limited due to the rarity of these diseases and the scant published clinical experience. The goal of this review was to create a comprehensive guide for nutritional management in CODE, based on the currently available literature, disease mechanism, and the PediCODE group experience. Enteral diet management in CODE can be divided into 3 distinct conceptual frameworks: nutrient elimination, nutrient supplementation, and generalized nutrient restriction. Response to nutrient elimination or supplementation can lead to resolution or significant improvement in the chronic diarrhea of CODE and resumption of normal growth. This pattern can be seen in CODE due to carbohydrate malabsorption, defects in fat absorption, and occasionally in electrolyte transport defects. In contrast, general diet restriction is mainly supportive. However, occasionally it allows parenteral nutrition weaning or reduction over time, mainly in enteroendocrine defects and rarely in epithelial trafficking and polarity defects. Further research is required to better elucidate the role of diet in the treatment of CODE and the appropriate diet management for each disease.
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Affiliation(s)
- Yaron Avitzur
- Group for Improvement of Intestinal Function and Treatment (GIFT), Transplant and Regenerative Centre, SickKids Hospital, Toronto, ON, Canada; Division of Gastroenterology, Hepatology and Nutrition, SickKids Hospital, University of Toronto, Toronto, ON, Canada.
| | - Lissette Jimenez
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States; Congenital Enteropathy Program, Boston Children's Hospital, Boston, MA, United States;; Harvard Digestive Disease Center, Boston MA, United States
| | - Inez Martincevic
- Division of Gastroenterology, Hepatology and Nutrition, SickKids Hospital, University of Toronto, Toronto, ON, Canada
| | - Sari Acra
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Glenda Courtney-Martin
- Group for Improvement of Intestinal Function and Treatment (GIFT), Transplant and Regenerative Centre, SickKids Hospital, Toronto, ON, Canada; Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Megan Gray
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Kayla Hope
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Aleixo Muise
- Division of Gastroenterology, Hepatology and Nutrition, SickKids Hospital, University of Toronto, Toronto, ON, Canada
| | - Paula M Prieto Jimenez
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital and the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Nancy Taylor
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States; Congenital Enteropathy Program, Boston Children's Hospital, Boston, MA, United States;; Harvard Digestive Disease Center, Boston MA, United States
| | - Martín G Martín
- Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital and the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
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4
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Ozturk M, Ates K, Esener Z, Mutlu H, Aydogmus C, Boztug K, Sarac H, Gezdirici A, Dogan M, Beser OF, Varol FI, Gokce IK, Ozdemir R, Tekedereli I. Expanding the phenotypic and genotypic characteristics of trichohepatoenteric syndrome: a report of eight patients from five unrelated families. Mol Biol Rep 2024; 51:736. [PMID: 38874671 DOI: 10.1007/s11033-024-09656-6] [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: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Trichohepatoenteric syndrome (THES) is characterized by neonatal-onset intractable diarrhea. It often requires long-term total parenteral nutrition (TPN). In addition, other characteristic findings of the syndrome include growth retardation, facial dysmorphism, hair abnormalities, various immunological problems and other rare system findings. Two genes and their associated pathogenic variants have been associated with this syndrome: SKIC3 and SKIC2. METHODS AND RESULTS In this case series, the clinical findings and molecular analysis results of a total of 8 patients from 5 different families who presented with persistent diarrhea and were diagnosed with THES were shared. Pathogenic variants were detected in the SKIC3 gene in 6 of our patients and in the SKIC2 gene in 2 patients. It was planned to compare the clinical findings of our patients with other patients, together with literature data, and to present yet-undefined phenotypic features that may be related to THES. In our case series, in addition to our patients with a novel variant, patient number 2 had a dual phenotype (THES and Spondyloepimetaphyseal dysplasia, sponastrime type) that has not been reported yet. Delay in gross motor skills, mild cognitive impairment, radioulnar synostosis, osteoporosis, nephropathy and cystic lesions (renal and liver) were observed as unreported phenotypic findings. CONCLUSIONS We are expanding the clinical and molecular repertoire of the syndrome regarding patients diagnosed with THES. We recommend that the NGS (next-generation sequencing) multigene panel should be used as a diagnostic tool in cases with persistent diarrhea.
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Affiliation(s)
- Murat Ozturk
- Department of Medical Genetics, Batman Education and Research Hospital, Batman, Turkey.
| | - Kubra Ates
- Department of Medical Genetics, Sakarya Education and Research Hospital, Sakarya, Turkey
| | - Zeynep Esener
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Hatice Mutlu
- Departments of Pediatric Genetics, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Cigdem Aydogmus
- Department of Pediatric Immunology and Allergy, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Kaan Boztug
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Lazarettgasse 14 AKH BT 25.3, Vienna, Austria
| | - Hatice Sarac
- Department of Medical Genetics, Inonu University Faculty of Medicine, Turgut Ozal Medical Center, Malatya, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Mustafa Dogan
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Omer Faruk Beser
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Cerrahpasa Faculty of Medicine, İstanbul University-Cerrahpasa, İstanbul, Turkey
| | - Fatma Ilknur Varol
- Departments of Pediatric Gastroenterology, Hepatology, and Nutrition, Faculty of Medicine, Inonu University, Malatya, Turkey
| | - Ismail Kursat Gokce
- Division of Neonatology, Department of Pediatrics, Inonu University School of Medicine, Malatya, Turkey
| | - Ramazan Ozdemir
- Division of Neonatology, Department of Pediatrics, Inonu University School of Medicine, Malatya, Turkey
| | - Ibrahim Tekedereli
- Department of Medical Genetics, Inonu University Faculty of Medicine, Turgut Ozal Medical Center, Malatya, Turkey
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5
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Yang K, Jeltema D, Yan N. Innate immune sensing of macromolecule homeostasis. Adv Immunol 2024; 161:17-51. [PMID: 38763701 DOI: 10.1016/bs.ai.2024.03.004] [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] [Indexed: 05/21/2024]
Abstract
The innate immune system uses a distinct set of germline-encoded pattern recognition receptors to recognize molecular patterns initially thought to be unique to microbial invaders, named pathogen-associated molecular patterns. The concept was later further developed to include similar molecular patterns originating from host cells during tissue damage, known as damage-associated molecular patterns. However, recent advances in the mechanism of monogenic inflammatory diseases have highlighted a much more expansive repertoire of cellular functions that are monitored by innate immunity. Here, we summarize several examples in which an innate immune response is triggered when homeostasis of macromolecule in the cell is disrupted in non-infectious or sterile settings. These ever-growing sensing mechanisms expand the repertoire of innate immune recognition, positioning it not only as a key player in host defense but also as a gatekeeper of cellular homeostasis. Therapeutics inspired by these advances to restore cellular homeostasis and correct the immune system could have far-reaching implications.
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Affiliation(s)
- Kun Yang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Devon Jeltema
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nan Yan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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6
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Zhang Y, Yang X, Guo S, Tao L, Xiang R, Huang H, Yang H. Exome sequencing analysis reveals two novel mutations in TTC37 in Chinese patients with Crohn's disease. QJM 2024; 117:145-147. [PMID: 37878822 DOI: 10.1093/qjmed/hcad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/19/2023] [Indexed: 10/27/2023] Open
Affiliation(s)
- Y Zhang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - X Yang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - S Guo
- Department of Cell Biology, School of Life Science, Central South University, Changsha, China
| | - L Tao
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - R Xiang
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- Department of Cell Biology, School of Life Science, Central South University, Changsha, China
| | - H Huang
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- Department of Cell Biology, School of Life Science, Central South University, Changsha, China
| | - H Yang
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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7
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Lee KY, Bremner R, Hartley J, Protheroe S, Haller W, Johnson T, Whyte L. Long term outcomes in children with trichohepatoenteric syndrome. Am J Med Genet A 2024; 194:141-149. [PMID: 37753667 DOI: 10.1002/ajmg.a.63409] [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: 07/12/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023]
Abstract
Trichohepatoenteric syndrome (THES) is a rare autosomal recessive disorder caused by mutations in either TTC37 or SKIV2L, usually leading to congenital diarrhea as part of a multisystem disease. Here, we report on the natural history of the disease for the largest UK cohort of patients with THES from 1996 to 2020. We systematically reviewed the clinical records and pathological specimens of patients diagnosed with THES managed in a single tertiary pediatric gastroenterology unit. Between 1996 and 2020, 13 patients (7 female and 6 male) were diagnosed with THES either by mutation analysis or by clinical phenotype. Two patients died from complications of infection. All patients received parenteral nutrition (PN) of which six patients were weaned off PN. All patients had gastrointestinal tract inflammation on endoscopy. Almost half of the cohort were diagnosed with monogenic inflammatory bowel disease (IBD) by the age of 11 years, confirmed by endoscopic and histological findings. Protracted diarrhea causing intestinal failure improves with time in all patients with THES, but monogenic IBD develops in later childhood that is refractory to conventional IBD treatments. Respiratory issues contribute to significant morbidity and mortality, and good respiratory care is crucial to prevent comorbidity.
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Affiliation(s)
- Kwang Yang Lee
- Department of Paediatric Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
- Department of Paediatric Gastroenterology and Nutrition, Bristol Royal Hospital for Children, Bristol, UK
| | - Ronald Bremner
- Department of Paediatric Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
| | - Jane Hartley
- Liver Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Sue Protheroe
- Department of Paediatric Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
| | - Wolfram Haller
- Department of Paediatric Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
- Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Tracey Johnson
- Department of Nutrition and Dietetics, Birmingham Children's Hospital, Birmingham, UK
| | - Lisa Whyte
- Department of Paediatric Gastroenterology and Nutrition, Birmingham Children's Hospital, Birmingham, UK
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Tomecki R, Drazkowska K, Kobylecki K, Tudek A. SKI complex: A multifaceted cytoplasmic RNA exosome cofactor in mRNA metabolism with links to disease, developmental processes, and antiviral responses. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1795. [PMID: 37384835 DOI: 10.1002/wrna.1795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
RNA stability and quality control are integral parts of gene expression regulation. A key factor shaping eukaryotic transcriptomes, mainly via 3'-5' exoribonucleolytic trimming or degradation of diverse transcripts in nuclear and cytoplasmic compartments, is the RNA exosome. Precise exosome targeting to various RNA molecules requires strict collaboration with specialized auxiliary factors, which facilitate interactions with its substrates. The predominant class of cytoplasmic RNA targeted by the exosome are protein-coding transcripts, which are carefully scrutinized for errors during translation. Normal, functional mRNAs are turned over following protein synthesis by the exosome or by Xrn1 5'-3'-exonuclease, acting in concert with Dcp1/2 decapping complex. In turn, aberrant transcripts are eliminated by dedicated surveillance pathways, triggered whenever ribosome translocation is impaired. Cytoplasmic 3'-5' mRNA decay and surveillance are dependent on the tight cooperation between the exosome and its evolutionary conserved co-factor-the SKI (superkiller) complex (SKIc). Here, we summarize recent findings from structural, biochemical, and functional studies of SKIc roles in controlling cytoplasmic RNA metabolism, including links to various cellular processes. Mechanism of SKIc action is illuminated by presentation of its spatial structure and details of its interactions with exosome and ribosome. Furthermore, contribution of SKIc and exosome to various mRNA decay pathways, usually converging on recycling of ribosomal subunits, is delineated. A crucial physiological role of SKIc is emphasized by describing association between its dysfunction and devastating human disease-a trichohepatoenteric syndrome (THES). Eventually, we discuss SKIc functions in the regulation of antiviral defense systems, cell signaling and developmental transitions, emerging from interdisciplinary investigations. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Kamil Kobylecki
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Tudek
- Laboratory of RNA Processing and Decay, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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9
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Munday RM, Haque R, Wojcik GL, Korpe P, Nayak U, Kirkpatrick BD, Petri WA, Duggal P. Genome-Wide Association Studies of Diarrhea Frequency and Duration in the First Year of Life in Bangladeshi Infants. J Infect Dis 2023; 228:979-989. [PMID: 36967705 PMCID: PMC11007397 DOI: 10.1093/infdis/jiad068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Diarrhea is the second leading cause of death in children under 5 years old worldwide. Known diarrhea risk factors include sanitation, water sources, and pathogens but do not fully explain the heterogeneity in frequency and duration of diarrhea in young children. We evaluated the role of host genetics in diarrhea. METHODS Using 3 well-characterized birth cohorts from an impoverished area of Dhaka, Bangladesh, we compared infants with no diarrhea in the first year of life to those with an abundance, measured by either frequency or duration. We performed a genome-wide association analysis for each cohort under an additive model and then meta-analyzed across the studies. RESULTS For diarrhea frequency, we identified 2 genome-wide significant loci associated with not having any diarrhea, on chromosome 21 within the noncoding RNA AP000959 (C allele odds ratio [OR] = 0.31, P = 4.01 × 10-8), and on chromosome 8 within SAMD12 (T allele OR = 0.35, P = 4.74 × 10-7). For duration of diarrhea, we identified 2 loci associated with no diarrhea, including the same locus on chromosome 21 (C allele OR = 0.31, P = 1.59 × 10-8) and another locus on chromosome 17 near WSCD1 (C allele OR = 0.35, P = 1.09 × 10-7). CONCLUSIONS These loci are in or near genes involved in enteric nervous system development and intestinal inflammation and may be potential targets for diarrhea therapeutics.
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Affiliation(s)
- Rebecca M Munday
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Poonum Korpe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Beth D Kirkpatrick
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - William A Petri
- Department of Medicine, Infectious Diseases, and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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10
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Babcock SJ, Flores-Marin D, Thiagarajah JR. The genetics of monogenic intestinal epithelial disorders. Hum Genet 2023; 142:613-654. [PMID: 36422736 PMCID: PMC10182130 DOI: 10.1007/s00439-022-02501-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022]
Abstract
Monogenic intestinal epithelial disorders, also known as congenital diarrheas and enteropathies (CoDEs), are a group of rare diseases that result from mutations in genes that primarily affect intestinal epithelial cell function. Patients with CoDE disorders generally present with infantile-onset diarrhea and poor growth, and often require intensive fluid and nutritional management. CoDE disorders can be classified into several categories that relate to broad areas of epithelial function, structure, and development. The advent of accessible and low-cost genetic sequencing has accelerated discovery in the field with over 45 different genes now associated with CoDE disorders. Despite this increasing knowledge in the causal genetics of disease, the underlying cellular pathophysiology remains incompletely understood for many disorders. Consequently, clinical management options for CoDE disorders are currently limited and there is an urgent need for new and disorder-specific therapies. In this review, we provide a general overview of CoDE disorders, including a historical perspective of the field and relationship to other monogenic disorders of the intestine. We describe the genetics, clinical presentation, and known pathophysiology for specific disorders. Lastly, we describe the major challenges relating to CoDE disorders, briefly outline key areas that need further study, and provide a perspective on the future genetic and therapeutic landscape.
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Affiliation(s)
- Stephen J Babcock
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Enders Rm 605, 300 Longwood Ave, Boston, MA, 02115, USA
| | - David Flores-Marin
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Enders Rm 605, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Enders Rm 605, 300 Longwood Ave, Boston, MA, 02115, USA.
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11
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Culbreath K, Keefe G, Nes E, Staffa SJ, Carey AN, Jaksic T, Goldsmith JD, Modi BP, Ouahed JD, Jimenez L. Factors Associated With Chronic Intestinal Inflammation Resembling Inflammatory Bowel Disease in Pediatric Intestinal Failure: A Matched Case-Control Study. J Pediatr Gastroenterol Nutr 2023; 76:468-474. [PMID: 36720109 DOI: 10.1097/mpg.0000000000003718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND AND AIMS There is a subset of intestinal failure patients with associated chronic intestinal inflammation resembling inflammatory bowel disease. This study aimed to evaluate factors associated with chronic intestinal inflammation in pediatric intestinal failure. METHODS This was a single-center retrospective case-control study of children <18 years old with intestinal failure. Cases were defined by abnormal amounts of chronic intestinal inflammation on biopsies. Children with diversion colitis, eosinophilic colitis, or isolated anastomotic ulceration were excluded. Cases were matched 1:2 to intestinal failure controls based on sex, etiology of intestinal failure, and duration of intestinal failure. Multivariable conditional logistic regression was used to compare clinical factors between cases and controls, accounting for clustering within matched sets. A subgroup analysis was performed assessing factors associated with escalation of anti-inflammatory therapy. RESULTS Thirty cases were identified and matched to 60 controls. On univariate analysis, longer parenteral nutrition (PN) duration (1677 vs 834 days, P = 0.03), current PN use (33.3% vs 20.0%, P = 0.037), and culture-proven bacterial overgrowth (53.3% vs 31.7%, P = 0.05) were associated with chronic intestinal inflammation. On multivariable analysis, no variable reached statistical significance. On subgroup analysis, duration of intestinal failure, location of inflammation, and worst degree of inflammation on histology were associated with escalation of therapy. CONCLUSIONS PN dependence and intestinal dysbiosis are associated with chronic intestinal inflammation in children with intestinal failure. Severity of inflammation is associated with escalation of therapy. Further analysis is needed to assess these associations and the efficacy of treatments in this population.
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Affiliation(s)
- Katherine Culbreath
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Gregory Keefe
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Emily Nes
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Steven J Staffa
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Alexandra N Carey
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Tom Jaksic
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Jeffrey D Goldsmith
- the Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Biren P Modi
- From the Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Jodie D Ouahed
- the Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Lissette Jimenez
- the Center for Advanced Intestinal Rehabilitation, Boston Children's Hospital and Harvard Medical School, Boston, MA
- the Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA
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12
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Moreno Traspas R, Teoh TS, Wong PM, Maier M, Chia CY, Lay K, Ali NA, Larson A, Al Mutairi F, Al-Sannaa NA, Faqeih EA, Alfadhel M, Cheema HA, Dupont J, Bézieau S, Isidor B, Low DY, Wang Y, Tan G, Lai PS, Piloquet H, Joubert M, Kayserili H, Kripps KA, Nahas SA, Wartchow EP, Warren M, Bhavani GS, Dasouki M, Sandoval R, Carvalho E, Ramos L, Porta G, Wu B, Lashkari HP, AlSaleem B, BaAbbad RM, Abreu Ferrão AN, Karageorgou V, Ordonez-Herrera N, Khan S, Bauer P, Cogne B, Bertoli-Avella AM, Vincent M, Girisha KM, Reversade B. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nat Genet 2022; 54:1214-1226. [PMID: 35864190 PMCID: PMC7615854 DOI: 10.1038/s41588-022-01120-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
Cirrhosis is usually a late-onset and life-threatening disease characterized by fibrotic scarring and inflammation that disrupts liver architecture and function. While it is typically the result of alcoholism or hepatitis viral infection in adults, its etiology in infants is much less understood. In this study, we report 14 children from ten unrelated families presenting with a syndromic form of pediatric liver cirrhosis. By genome/exome sequencing, we found recessive variants in FOCAD segregating with the disease. Zebrafish lacking focad phenocopied the human disease, revealing a signature of altered messenger RNA (mRNA) degradation processes in the liver. Using patient's primary cells and CRISPR-Cas9-mediated inactivation in human hepatic cell lines, we found that FOCAD deficiency compromises the SKI mRNA surveillance pathway by reducing the levels of the RNA helicase SKIC2 and its cofactor SKIC3. FOCAD knockout hepatocytes exhibited lowered albumin expression and signs of persistent injury accompanied by CCL2 overproduction. Our results reveal the importance of FOCAD in maintaining liver homeostasis and disclose a possible therapeutic intervention point via inhibition of the CCL2/CCR2 signaling axis.
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Affiliation(s)
- Ricardo Moreno Traspas
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Tze Shin Teoh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pui-Mun Wong
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Michael Maier
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Crystal Y Chia
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Kenneth Lay
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Nur Ain Ali
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Austin Larson
- Section of Pediatrics-Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Fuad Al Mutairi
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | | | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Department of Genetics and Precision Medicine, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Medical Genomic Research, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Huma Arshad Cheema
- Division of Pediatric Gastroenterology-Hepatology and Nutrition, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Juliette Dupont
- Department of Pediatrics, Genetic Services, Lisbon North University Hospital Center, Lisbon, Portugal
| | - Stéphane Bézieau
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Bertrand Isidor
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Dorrain Yanwen Low
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Grace Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hugues Piloquet
- Gastropediatrics Department, Nantes University Hospital Center, Nantes, France
| | - Madeleine Joubert
- Anatomopathology Department, Nantes University Hospital Center, Nantes, France
| | - Hulya Kayserili
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
| | - Kimberly A Kripps
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric P Wartchow
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, CO, USA
| | - Mikako Warren
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Majed Dasouki
- Department of Pediatric Genetics, AdventHealth Medical Group, Orlando, FL, USA
| | - Renata Sandoval
- Department of Oncogenetics, Hospital Sírio-Libanês, Brasília, Brazil
| | - Elisa Carvalho
- Department of Pediatric Gastroenterology and Hepatology, Hospital da Criança de Brasília José Alencar, UniCEUB, Brasília, Brazil
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo, Brazil
| | - Gilda Porta
- Department of Pediatric Hepatology, Transplant Unit, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College, Mangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Badr AlSaleem
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Raeda M BaAbbad
- Section of Pediatric Gastroenterology-Hepatology, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Benjamin Cogne
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | | | - Marie Vincent
- Medical Genetics Service, Nantes University Hospital Center, Nantes, France
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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13
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Yang K, Han J, Gill JG, Park JY, Sathe MN, Gattineni J, Wright T, Wysocki C, de la Morena MT, Yan N. The mammalian SKIV2L RNA exosome is essential for early B cell development. Sci Immunol 2022; 7:eabn2888. [PMID: 35658009 PMCID: PMC9376044 DOI: 10.1126/sciimmunol.abn2888] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The SKIV2L RNA exosome is an evolutionarily conserved RNA degradation complex in the eukaryotes. Mutations in the SKIV2L gene are associated with a severe inherited disorder, trichohepatoenteric syndrome (THES), with multisystem involvement but unknown disease mechanism. Here, we reported a THES patient with SKIV2L mutations showing severe primary B cell immunodeficiency, hypogammaglobulinemia, and kappa-restricted plasma cell dyscrasia but normal T cell and NK cell function. To corroborate these findings, we made B cell-specific Skiv2l knockout mice (Skiv2lfl/flCd79a-Cre), which lacked both conventional B-2 and innate-like B-1 B cells in the periphery and secondary lymphoid organs. This was linked to a requirement of SKIV2L RNA exosome activity in the bone marrow during early B cell development at the pro-B cell to large pre-B cell transition. Mechanistically, Skiv2l-deficient pro-B cells exhibited cell cycle arrest and DNA damage. Furthermore, loss of Skiv2l led to substantial out-of-frame V(D)J rearrangement of immunoglobulin heavy chain and severely reduced surface expression of μH, both of which are crucial for pre-BCR signaling and proliferative burst during early B cell development. Together, our data demonstrated a crucial role for SKIV2L RNA exosome in early B cell development in both human and mice by ensuring proper V(D)J recombination and Igh expression, which serves as the molecular basis for immunodeficiency associated with THES.
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Affiliation(s)
- Kun Yang
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jie Han
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jennifer G. Gill
- Department of Dermatology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jason Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Meghana N. Sathe
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jyothsna Gattineni
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tracey Wright
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christian Wysocki
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - M. Teresa de la Morena
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children's Hospital, Seattle, WA, USA
| | - Nan Yan
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, USA
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14
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Orlando LJ, Yim MK, Hallmark T, Cotner M, Johnson SJ, van Hoof A. A yeast model for trichohepatoenteric syndrome suggests strong loss of Ski2 function in most causative mutations. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000575. [PMID: 35607352 PMCID: PMC9123431 DOI: 10.17912/micropub.biology.000575] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
Abstract
The intestinal and immune disorder trichohepatoenteric syndrome (THES) is characterized by mutations in human Ski2 and Ski3, also known as SKIV2L and TTC37, respectively. The mechanism by which these mutations leads to the immunodeficiency, chronic diarrhea, failure to thrive and liver disease associated with THES is unknown. To what degree THES patient mutations in Ski2 affect Ski2 function and how the differences in Ski2 function could lead to varying patient outcomes has not been studied. Here, we assayed function of THES ski2 mutants in the yeast homolog. Our results show that most THES patient mutations cause severe dysfunction in Ski2. This provides the first functional analysis of these mutations and suggests that the yeast assay may be helpful in distinguishing between pathological and benign variants.
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Affiliation(s)
- Luisa J Orlando
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston and The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston
| | - Matthew K Yim
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah
| | - Thomson Hallmark
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah
| | - Michael Cotner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah
| | - Sean J Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston and The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston
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15
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Yang M, Jiang Y, Shao X. Case Report: A Novel Homozygous Frameshift Mutation of the SKIV2L Gene in a Trichohepatoenteric Syndrome Patient Presenting With Short Stature, Premature Ovarian Failure, and Osteoporosis. Front Genet 2022; 13:879899. [PMID: 35571060 PMCID: PMC9094698 DOI: 10.3389/fgene.2022.879899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Trichohepatoenteric syndrome (THES) is a rare Mendelian autosomal recessive genetic disease characterized by intractable diarrhea, woolly hair, facial abnormality, immune dysfunction, and intrauterine growth restriction. THES mutations are found in the TTC37 and SKIV2L genes, which encode two components of the human superkiller (SKI) complex. Methods and results: We report one case of a 32-year-old woman of Chinese descent with THES, who was born with a low weight (2000 g). She had intractable diarrhea during the neonatal period and was allergic to cow’s milk and condensed milk, but did not require total parenteral nutrition. She experienced menarche at age 12 and amenorrhea at age 28. In May 2019, the patient presented with a left fibular head fracture and was diagnosed with osteoporosis. Genetic testing showed a novel mutation in exon1 [p.E5Afs∗37 (c.12_13del)] of SKIV2L, which is composed of 28 exons. After the diagnosis, hormone replacement therapy was prescribed, in addition to the routine calcium and vitamin D supplements. Conclusion: This case expands the clinical characteristic and phenotype spectrum of THES, providing further understanding of SKIV2L and its autoimmune influence.
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Affiliation(s)
- Minyi Yang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Jiang
- Department of Endocrinology and Metabolism, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
| | - Xinyu Shao
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Endocrinology and Metabolism, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, China
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16
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Lin B, Goldbach-Mansky R. Pathogenic insights from genetic causes of autoinflammatory inflammasomopathies and interferonopathies. J Allergy Clin Immunol 2022; 149:819-832. [PMID: 34893352 PMCID: PMC8901451 DOI: 10.1016/j.jaci.2021.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/31/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022]
Abstract
A number of systemic autoinflammatory diseases arise from gain-of-function mutations in genes encoding IL-1-activating inflammasomes or cytoplasmic nucleic acid sensors including the receptor and sensor STING and result in increased IL-1 and type I interferon production, respectively. Blocking these pathways in human diseases has provided proof-of-concept, confirming the prominent roles of these cytokines in disease pathogenesis. Recent insights into the multilayered regulation of these sensor pathways and insights into their role in amplifying the disease pathogenesis of monogenic and complex genetic diseases spurred new drug development targeting the sensors. This review provides insights into the pathogenesis and genetic causes of these "prototypic" diseases caused by gain-of function mutations in IL-1-activating inflammasomes (inflammasomopathies) and in interferon-activating pathways (interferonopathies) including STING-associated vasculopathy with onset in infancy, Aicardi-Goutieres syndrome, and proteasome-associated autoinflammatory syndromes that link activation of the viral sensors STING, "self" nucleic acid metabolism, and the ubiquitin-proteasome system to "type I interferon production" and human diseases. Clinical responses and biomarker changes to Janus kinase inhibitors confirm a role of interferons, and a growing number of diseases with "interferon signatures" unveil extensive cross-talk between major inflammatory pathways. Understanding these interactions promises new tools in tackling the significant clinical challenges in treating patients with these conditions.
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Affiliation(s)
- Bin Lin
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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17
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Yang K, Han J, Asada M, Gill JG, Park JY, Sathe MN, Gattineni J, Wright T, Wysocki CA, de la Morena MT, Garza LA, Yan N. Cytoplasmic RNA quality control failure engages mTORC1-mediated autoinflammatory disease. J Clin Invest 2022; 132:e146176. [PMID: 35040435 PMCID: PMC8759780 DOI: 10.1172/jci146176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
Inborn errors of nucleic acid metabolism often cause aberrant activation of nucleic acid sensing pathways, leading to autoimmune or autoinflammatory diseases. The SKIV2L RNA exosome is cytoplasmic RNA degradation machinery that was thought to be essential for preventing the self-RNA-mediated interferon (IFN) response. Here, we demonstrate the physiological function of SKIV2L in mammals. We found that Skiv2l deficiency in mice disrupted epidermal and T cell homeostasis in a cell-intrinsic manner independently of IFN. Skiv2l-deficient mice developed skin inflammation and hair abnormality, which were also observed in a SKIV2L-deficient patient. Epidermis-specific deletion of Skiv2l caused hyperproliferation of keratinocytes and disrupted epidermal stratification, leading to impaired skin barrier with no appreciable IFN activation. Moreover, Skiv2l-deficient T cells were chronically hyperactivated and these T cells attacked lesional skin as well as hair follicles. Mechanistically, SKIV2L loss activated the mTORC1 pathway in both keratinocytes and T cells. Both systemic and topical rapamycin treatment of Skiv2l-deficient mice ameliorated epidermal hyperplasia and skin inflammation. Together, we demonstrate that mTORC1, a classical nutrient sensor, also senses cytoplasmic RNA quality control failure and drives autoinflammatory disease. We also propose SKIV2L-associated trichohepatoenteric syndrome (THES) as a new mTORopathy for which sirolimus may be a promising therapy.
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Affiliation(s)
- Kun Yang
- Department of Immunology and
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jie Han
- Department of Immunology and
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Mayumi Asada
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jason Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development
| | | | | | | | - Christian A. Wysocki
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - M. Teresa de la Morena
- Department of Pediatrics, University of Washington and
- Seattle Children’s Hospital, Seattle, Washington, USA
| | - Luis A. Garza
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nan Yan
- Department of Immunology and
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas, USA
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18
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Abstract
Loss-of-function mutations in SKIV2L underlie trichohepatoenteric syndrome (THES2), a rare inborn error of immunity characterized by diarrhea, skin lesions, brittle hair, and immunodeficiency. SKIV2L is part of a multiprotein complex required for exosome-mediated RNA surveillance through RNA decay. In this issue of the JCI, Yang et al. delineate a mechanism underlying autoinflammatory skin disease in Skiv2l-deficient mice. Thus, a lack of SKIV2L activates mTORC1 signaling in keratinocytes and T cells, impeding skin barrier integrity and T cell homeostasis. Interestingly, treatment with the mTOR inhibitor rapamycin improves skin symptoms in Skiv2l-deficient mice, suggesting a possible therapeutic avenue for patients with THES2.
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19
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Goulet O, Pigneur B, Charbit-Henrion F. Congenital enteropathies involving defects in enterocyte structure or differentiation. Best Pract Res Clin Gastroenterol 2022; 56-57:101784. [PMID: 35331396 DOI: 10.1016/j.bpg.2021.101784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023]
Abstract
Congenital enteropathies (CE) are a group of rare inherited diseases with a typical onset early in life. They involve defects in enterocyte structure or differentiation. They can cause a severe condition of intestinal failure (IF). The diagnostic approach is based first on clinical presentation (consanguinity, prenatal expression, polyhydramnios, early neonatal onset, aspect of stools, persistence at bowel rest, associated extra-digestive manifestations….) and histo-pathological analyses. These rare intestinal diseases cause protracted diarrhea that might resolve, for a few, with a dietetic approach. However, protracted or permanent IF may require long term parenteral nutrition and, in limited cases, intestinal transplantation. With the progresses in both clinical nutrition and genetics, many of these CE are nowadays associated with recognized gene mutations. It improved our knowledge and the understanding in the patho-physiology of these diseases, thus, leading potentially to therapeutic perspectives. These review cover most of the early onset CE and excludes the immune related diarrhea.
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Affiliation(s)
- Olivier Goulet
- Division of Paediatric Gastroenterology Hepatology and Nutrition, University Paris-Centre, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France.
| | - Bénédicte Pigneur
- Division of Paediatric Gastroenterology Hepatology and Nutrition, University Paris-Centre, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France
| | - Fabienne Charbit-Henrion
- Department of Genetics, Hôpital Necker-Enfants Malades, 149, Rue de Sèvres, 75743, PARIS Cedex 15, France
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20
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Albar RF, Alghamdi MS, Alsulimani EF, Almasrahi AM, Alsalmi KA. A Case of Mild Trichohepatoenteric Syndrome With New Variant Mutation in SKIV2L Gene: Case Report. Cureus 2021; 13:e19404. [PMID: 34926006 PMCID: PMC8654094 DOI: 10.7759/cureus.19404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/05/2022] Open
Abstract
Trichohepatoenteric syndrome (THES) is a rare autosomal recessive genetic disease characterized by severe early onset diarrhea, woolly and brittle hair, immunodeficiency, and liver disease. A mutation in either SKIV2L or TTC37 genes can cause the disease. We report a case of a 41-month-old girl who suffered from intractable watery diarrhea, hair abnormality, dysmorphic features, and poor weight gain. The diagnosis was made through whole-exome sequencing analysis. The analysis detected a new variant mutation (c.1201G > A) p. (Glu401Lys) in the SKIV2L gene. She was admitted once for poor weight gain and nasogastric tube (NGT) feeding, with which the patient showed improvement. She was discharged to go home on hypoallergenic baby formulas and a regular diet with improved weight gain.
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Affiliation(s)
- Rawia F Albar
- Pediatrics, King Abdulaziz Medical City, Jeddah, SAU
| | - Mohammed S Alghamdi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, SAU
| | - Enad F Alsulimani
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, SAU
| | - Ahmed M Almasrahi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, SAU
| | - Khalid A Alsalmi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, SAU
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21
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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22
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Mantoo MR, Malik R, Das P, Yadav R, Nakra T, Chouhan P. Congenital Diarrhea and Enteropathies in Infants: Approach to Diagnosis. Indian J Pediatr 2021; 88:1135-1138. [PMID: 34292522 DOI: 10.1007/s12098-021-03844-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/04/2021] [Indexed: 10/20/2022]
Abstract
Congenital diarrhea and enteropathies (CODEs) are monogenic disorders causing early onset of intractable diarrhea. Their diagnosis and management are challenging. With the availability of commercial next generation genetic testing, we are now better able to classify and manage these disorders. The authors present their experience with 4 cases. Two patients had congenital tufting enteropathy (CTE) and 1 case each of microvillous inclusion disease (MVID) and trichohepatoenteric syndrome (THES). Age at onset varied from 3 to 38 d of life. Light microscopy and electron microscopy of duodenal and rectal endoscopic biopsies were consistent with the diagnosis. Genetic evaluation was possible in 3 cases indicating causative mutations. Two children (CTE and MVID) were alive at last follow-up. The authors suggest a stepwise approach to the diagnosis and management of these disorders in the Indian context.
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Affiliation(s)
- Mohsin Raj Mantoo
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rohan Malik
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India.
| | - Prasenjit Das
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rajni Yadav
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tripti Nakra
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pandu Chouhan
- Departments of Pediatrics and Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
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Zhang Q, Qian X, Zhou J, Han L, Zhou S, Wang Z. Case Report: Novel Compound-Heterozygous Variants of SKIV2L Gene that Cause Trichohepatoenteric Syndrome 2. Front Genet 2021; 12:756451. [PMID: 34691159 PMCID: PMC8527088 DOI: 10.3389/fgene.2021.756451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/17/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Trichohepatoenteric syndrome (THES) is a rare disease that mainly causes intractable diarrhea. It is classified into THES1 and THES2, which are associated with the tetratricopeptide repeat domain 37 (TTC37) gene and Ski2-like RNA helicase (SKIV2L) gene, respectively. THES is not very prevalent in China or worldwide, but new cases have increasingly been reported. Methods and Results: Here, we report the clinical and genetic information of a 1.5-month-old girl who was admitted to our hospital due to diarrhea and failure to thrive. Whole-exome sequencing (WES) revealed novel compound-heterozygous variants of the SKIV2L gene, c.3602_3609delAGCGCCTG (p.Q1201Rfs*2), and c.1990A > G (p.T664A) as the causative factors, which were confirmed via Sanger sequencing. Upon continuous feeding with an amino-acid formula through a gastric tube and parenteral nutrition, the patient resumed thriving and her stool frequency decreased. Conclusion: We report a girl carrying novel variants of the SKIV2L gene that cause THES2, thereby providing valuable information on the diagnosis of THES2 and expanding the spectrum of disease-causing SKIV2L mutations.
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Affiliation(s)
- Qiao Zhang
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xia Qian
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Jianli Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Lin Han
- Running Gene Inc., Beijing, China
| | - Shaoming Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Zhaoxia Wang
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
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24
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Alsaleem BM, Hasosah M, Ahmed ABM, Al Hatlani MM, Alanazi AH, Al-Hussaini A, Asery AT, Alghamdi KA, AlRuwaithi MM, Khormi MAM, Al Sarkhy A, Alshamrani AS. Tricho-hepato-enteric syndrome: Retrospective multicenter experience in Saudi Arabia. Saudi J Gastroenterol 2021; 28:135-142. [PMID: 34414925 PMCID: PMC9007078 DOI: 10.4103/sjg.sjg_200_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Trichohepatoenteric syndrome (THES) is a very rare disorder that is characterized by intractable congenital diarrhea, woolly hair, intrauterine growth restriction, facial dysmorphism, and short stature. Our knowledge of THES is limited due to the small number of reported cases. METHODS Thirty patients diagnosed with THES, all molecularly confirmed by whole exome sequencing (WES) to have biallelic variants in TTC37 or SKIV2L, were included in the study. Clinical, biochemical, and nutritional phenotypes and outcome data were collected from all participants. RESULTS The median age of THES patients was 3.7 years (0.9-23 years). Diarrhea and malnutrition were the most common clinical features (100%). Other common features included hair abnormalities (96%), skin hyperpigmentation (87%), facial dysmorphic abnormalities (73%), psychomotor retardation (57%), and hepatic abnormalities (30%). Twenty-five patients required parenteral nutrition (83%) with a mean duration of 13.34 months, and nearly half were eventually weaned off. Parenteral nutrition was associated with a poor prognosis. The vast majority of cases (89.6%) had biallelic variants in SKIV2L, with biallelic variants in TTC37 accounting for the remaining cases. A total of seven variants were identified in TTC37 (n = 3) and SKIV2L (n = 4). The underlying genotype influenced some phenotypic aspects, especially liver involvement, which was more common in TTC37-related THES. CONCLUSION Our data helps define the natural history of THES and provide clinical management guidelines.
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Affiliation(s)
- Badr M. Alsaleem
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia,Address for correspondence: Dr. Badr M. Alsaleem, Pediatric Consultant Gastroenterologist, King Fahad Medical City, Children's Hospital, Intestinal Failure Program, Riyadh, Saudi Arabia. E-mail:
| | - Mohammed Hasosah
- Department of Pediatric Gastroenterology, King Abdulaziz Medical City, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Amna Basheer M. Ahmed
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Maher M. Al Hatlani
- Department of Pediatric Gastroenterology, IABF Hospital of National Guard, Dammam, Saudi Arabia
| | - Aziz Helal Alanazi
- Department of Pediatric Gastroenterology, King Abdulaziz Medical City, Ministry of National Guard, Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman Al-Hussaini
- The Division of Pediatric Gastroenterology, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia,Alfaisal University, College of Medicine, Riyadh, Saudi Arabia,Prince Abdullah bin Khalid Celiac Disease Research Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali T. Asery
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Khalid A. Alghamdi
- Department of Pediatric Gastroenterology, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Muhanad M. AlRuwaithi
- Department of Pediatric Gastroenterology, Intestinal Failure Program, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Musa Ali M. Khormi
- Department of Pediatric Gastroenterology, King Saud Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al Sarkhy
- Department of Pediatric Gastroenterology, King Khalid University Hospital, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ali S. Alshamrani
- Department of Pediatric Gastroenterology, Maternity and Children's Hospital, Makkah, Saudi Arabia
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25
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Genetic Enteropathies Linked to Epithelial Structural Abnormalities and Enteroendocrine Deficiency: A Systematic Review. J Pediatr Gastroenterol Nutr 2021; 72:826-832. [PMID: 33976085 DOI: 10.1097/mpg.0000000000003049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Congenital diarrhea and enteropathies linked to epithelial structural abnormalities constitute 3 different rare diseases: the tufting enteropathies (TE; EPCAM and SPINT2 mutations), microvillous inclusion disease (MVID; MYO5B and STX3 mutations), and tricho-hepato-enteric syndrome (THE; TTC37 and SKIV2L mutations). Moreover, enteroendocrine deficiencies (ED; PCSK1 and NEUROG3 mutations) share common clinical characteristics with TE, THE, and MVID in that the treatment requires, in most cases, long-term parenteral nutrition. Although numerous cases have been reported in the literature, aggregated data on morbidity and mortality are missing owing to the rarity of the diseases. METHODS We performed a systematic review of all published cases and retrieved 86 articles describing 323 patients (164 boys and 135 girls). RESULTS The mortality rate was 20.28%, with a median age at death of 13.5 months (range 0-228 months); the mortality risk was 30.8/1000 person-year; in half of the cases, death was caused by infections. Parenteral nutrition was required in 95.4% of patients and weaning off from parenteral nutrition was achieved in 29.35% at a median age of 23 months (range 3.3-276 months). The patients with ED linked to PCSK1 were nearly all weaned at a median age of 14 months, but most of the patients became overweight. MVID patients with MYO5B mutations were most often born preterm. ED linked to NEUROG3 mutation and THE patients usually presented with intrauterine growth retardation. CONCLUSIONS This review presents data from 323 patients with congenital diarrhea linked to EPCAM TE, SPINT2 TE, TTC37 THE, SKIV2L THE, MYO5B MVID, STX3 MVID, NEUROG3 ED, and PCSK1 ED mutations.
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26
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Dorum S, Gorukmez O. Expanding the clinical spectrum in trichohepatoenteric syndrome. Am J Med Genet A 2021; 185:2873-2877. [PMID: 34037310 DOI: 10.1002/ajmg.a.62354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 11/05/2022]
Abstract
Trichohepatoenteric syndrome (THES) is a very rare autosomal recessive genetic disorder, which is characterized by intractable diarrhea during infancy, dysmorphic features, immunodeficiency, and a failure to thrive. There are still significant difficulties for patients and clinicians in terms of the management of THES, even though its molecular basis has been uncovered in the last decade. In this article, we have presented two cases relating to siblings that have been diagnosed with the condition. Concerning one of the patients, we described a novel variation (c.2114 + 5G > A) in the TTC37 gene and a mild clinical course; meanwhile, the other one was clinically diagnosed with THES at 17 years of age, but they had seizures and died suddenly. These cases expand the spectrum of clinical findings in relation to THES.
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Affiliation(s)
- Sevil Dorum
- Division of Metabolism, Department of Pediatrics, University of Health Sciences, Bursa Yuksek Ihtisas Training and Research Hospital, Bursa, Turkey
| | - Ozlem Gorukmez
- Department of Genetics, University of Health Sciences, Bursa Yuksek Ihtisas Training and Research Hospital, Bursa, Turkey
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27
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Somashekar PH, Kaur P, Stephen J, Guleria VS, Kadavigere R, Girisha KM, Bielas S, Upadhyai P, Shukla A. Bi-allelic missense variant, p.Ser35Leu in EXOSC1 is associated with pontocerebellar hypoplasia. Clin Genet 2021; 99:594-600. [PMID: 33463720 PMCID: PMC9990822 DOI: 10.1111/cge.13928] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
RNA exosome is a highly conserved ribonuclease complex essential for RNA processing and degradation. Bi-allelic variants in exosome subunits EXOSC3, EXOSC8 and EXOSC9 have been reported to cause pontocerebellar hypoplasia type 1B, type 1C and type 1D, respectively, while those in EXOSC2 cause short stature, hearing loss, retinitis pigmentosa and distinctive facies. We ascertained an 8-months-old male with developmental delay, microcephaly, subtle dysmorphism and hypotonia. Pontocerebellar hypoplasia and delayed myelination were noted on neuroimaging. A similarly affected elder sibling succumbed at the age of 4-years 6-months. Chromosomal microarray returned normal results. Exome sequencing revealed a homozygous missense variant, c.104C > T p.(Ser35Leu) in EXOSC1 (NM_016046.5) as the possible candidate. In silico mutagenesis revealed loss of a polar contact with neighboring Leu37 residue. Quantitative real-time PCR indicated no appreciable differences in EXOSC1 transcript levels. Immunoblotting and blue native PAGE revealed reduction in the EXOSC1 protein levels and EXO9 complex in the proband, respectively. We herein report an individual with the bi-allelic variant c.104C>T p.(Ser35Leu) in EXOSC1 and clinical features of pontocerebellar hypoplasia type 1. Immunoblotting and blue native PAGE provide evidence for the pathogenicity of the variant. Thus, we propose EXOSC1 as a novel candidate gene for pontocerebellar hypoplasia.
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Affiliation(s)
- Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Joshi Stephen
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Vishal Singh Guleria
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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28
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Uhlig HH, Charbit-Henrion F, Kotlarz D, Shouval DS, Schwerd T, Strisciuglio C, de Ridder L, van Limbergen J, Macchi M, Snapper SB, Ruemmele FM, Wilson DC, Travis SP, Griffiths AM, Turner D, Klein C, Muise AM, Russell RK. Clinical Genomics for the Diagnosis of Monogenic Forms of Inflammatory Bowel Disease: A Position Paper From the Paediatric IBD Porto Group of European Society of Paediatric Gastroenterology, Hepatology and Nutrition. J Pediatr Gastroenterol Nutr 2021; 72:456-473. [PMID: 33346580 PMCID: PMC8221730 DOI: 10.1097/mpg.0000000000003017] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND It is important to identify patients with monogenic IBD as management may differ from classical IBD. In this position statement we formulate recommendations for the use of genomics in evaluating potential monogenic causes of IBD across age groups. METHODS The consensus included paediatric IBD specialists from the Paediatric IBD Porto group of the European Society of Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) and specialists from several monogenic IBD research consortia. We defined key topics and performed a systematic literature review to cover indications, technologies (targeted panel, exome and genome sequencing), gene panel setup, cost-effectiveness of genetic screening, and requirements for the clinical care setting. We developed recommendations that were voted upon by all authors and Porto group members (32 voting specialists). RESULTS We recommend next-generation DNA-sequencing technologies to diagnose monogenic causes of IBD in routine clinical practice embedded in a setting of multidisciplinary patient care. Routine genetic screening is not recommended for all IBD patients. Genetic testing should be considered depending on age of IBD-onset (infantile IBD, very early-onset IBD, paediatric or young adult IBD), and further criteria, such as family history, relevant comorbidities, and extraintestinal manifestations. Genetic testing is also recommended in advance of hematopoietic stem cell transplantation. We developed a diagnostic algorithm that includes a gene panel of 75 monogenic IBD genes. Considerations are provided also for low resource countries. CONCLUSIONS Genomic technologies should be considered an integral part of patient care to investigate patients at risk for monogenic forms of IBD.
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Affiliation(s)
- Holm H. Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Fabienne Charbit-Henrion
- Université de Paris, INSERM UMR 1163 Immunité Intestinale, APHP, Hôpital Necker Enfants Malades, Service de Génétique moléculaire, Paris, France
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dror S. Shouval
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | | | - Lissy de Ridder
- Department of Paediatric Gastroenterology, Erasmus University Medical Center Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Johan van Limbergen
- Amsterdam University Medical Centres, Emma Children’s Hospital, The Netherlands and Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Marina Macchi
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Frank M. Ruemmele
- Université de Paris, APHP, Hôpital Necker Enfants Malades, Service de Gastroentérologie pédiatrique, Paris, France
| | - David C. Wilson
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
| | - Simon P.L. Travis
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
- Biomedical Research Center, University of Oxford, Oxford, United Kingdom
| | - Anne M. Griffiths
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Dan Turner
- Shaare Zedek Medical Center, The Hebrew University of Jerusalem, Israel
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Aleixo M. Muise
- The Hospital for Sick Children, University of Toronto
- SickKids Inflammatory Bowel Disease Centre and Cell Biology Program, Research Institute, The Hospital for Sick Children
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Toronto, Ontario, Canada
| | - Richard K. Russell
- Child Life and Health, University of Edinburgh, Department of Paediatric Gastroenterology, The Royal Hospital for Sick Children, Edinburgh
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29
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Morgan NV, Yngvadottir B, O'Driscoll M, Clark GR, Walsh D, Martin E, Tee L, Reid E, Titheradge HL, Maher ER. Evidence that autosomal recessive spastic cerebral palsy-1 (CPSQ1) is caused by a missense variant in HPDL. Brain Commun 2021; 3:fcab002. [PMID: 33634263 PMCID: PMC7892364 DOI: 10.1093/braincomms/fcab002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/15/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023] Open
Abstract
A subset of individuals diagnosed with cerebral palsy will have an underlying genetic diagnosis. Previously, a missense variant in GAD1 was described as a candidate mutation in a single family diagnosed with autosomal recessive spastic cerebral palsy-1 (CPSQ1; OMIM 603513). Following the ascertainment of a further branch of the CPSQ1 kindred, we found that the previously reported GAD1 variant did not segregate with the neurological disease phenotype in the recently ascertained branch of the kindred. Following genetic linkage studies to map autozygous regions and whole-exome sequencing, a missense variant (c.527 T > C; p. Leu176Pro, rs773333490) in the HPDL gene was detected and found to segregate with disease status in both branches of the kindred. HPDL encodes a 371-amino acid protein (4-Hydroxyphenylpyruvate Dioxygenase Like) that localizes to mitochondria but whose function is uncertain. Recently, biallelic loss of function variants and missense substitution-causing variants in HPDL were reported to cause a childhood onset progressive spastic movement disorder with a variable presentation. These findings suggest that HPDL-related neurological disease may mimic spastic cerebral palsy and that GAD1 should not be included in diagnostic gene panels for inherited cerebral palsy.
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Affiliation(s)
- Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Bryndis Yngvadottir
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Mary O'Driscoll
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's NHS Trust, Birmingham B15 2TG, UK
| | - Graeme R Clark
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Diana Walsh
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Trust, Birmingham B15 2TG, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK.,Oncology Department, Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Louise Tee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Evan Reid
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK.,Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Hannah L Titheradge
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's NHS Trust, Birmingham B15 2TG, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
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30
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Aguilar LC, Paul B, Reiter T, Gendron L, Arul Nambi Rajan A, Montpetit R, Trahan C, Pechmann S, Oeffinger M, Montpetit B. Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2. Nucleic Acids Res 2020; 48:11675-11694. [PMID: 33137177 PMCID: PMC7672433 DOI: 10.1093/nar/gkaa964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.
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Affiliation(s)
- Lisbeth-Carolina Aguilar
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Biplab Paul
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
| | - Louis Gendron
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
| | - Christian Trahan
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Sebastian Pechmann
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Department for Systems Biology, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada
- Food Science Graduate Group, University of California Davis, Davis, CA, USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis, Davis, CA, USA
- Department of Viticulture and Enology, University of California Davis, Davis, CA, USA
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31
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Weick EM, Lima CD. RNA helicases are hubs that orchestrate exosome-dependent 3'-5' decay. Curr Opin Struct Biol 2020; 67:86-94. [PMID: 33147539 DOI: 10.1016/j.sbi.2020.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 01/10/2023]
Abstract
The RNA exosome is a conserved complex of proteins that mediates 3'-5' RNA processing and decay. Its functions range from processing of non-coding RNAs such as ribosomal RNAs and decay of aberrant transcripts in the nucleus to cytoplasmic mRNA turnover and quality control. Ski2-like RNA helicases translocate substrates to exosome-associated ribonucleases and interact with the RNA exosome either directly or as part of multi-subunit helicase-containing complexes that identify and target RNA substrates for decay. Recent structures of these helicases with their RNA-binding partners or the RNA exosome have advanced our understanding of a system of modular and mutually exclusive contacts between the exosome and exosome-associated helicase complexes that shape the transcriptome by orchestrating exosome-dependent 3'-5' decay.
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Affiliation(s)
- Eva-Maria Weick
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.
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32
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Wu D, Dean J. EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes. Nucleic Acids Res 2020; 48:5349-5365. [PMID: 32313933 DOI: 10.1093/nar/gkaa249] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/28/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Growing mammalian oocytes accumulate substantial amounts of RNA, most of which is degraded during subsequent meiotic maturation. The growth-to-maturation transition begins with germinal vesicle or nuclear envelope breakdown (GVBD) and is critical for oocyte quality and early development. The molecular machinery responsible for the oocyte transcriptome transition remains unclear. Here, we report that an exosome-associated RNase, EXOSC10, sculpts the transcriptome to facilitate the growth-to-maturation transition of mouse oocytes. We establish an oocyte-specific conditional knockout of Exosc10 in mice using CRISPR/Cas9 which results in female subfertility due to delayed GVBD. By performing multiple single oocyte RNA-seq, we document dysregulation of several types of RNA, and the mRNAs that encode proteins important for endomembrane trafficking and meiotic cell cycle. As expected, EXOSC10-depleted oocytes have impaired endomembrane components including endosomes, lysosomes, endoplasmic reticulum and Golgi. In addition, CDK1 fails to activate, possibly due to persistent WEE1 activity, which blocks lamina phosphorylation and disassembly. Moreover, we identified rRNA processing defects that cause higher percentage of developmentally incompetent oocytes after EXOSC10 depletion. Collectively, we propose that EXOSC10 promotes normal growth-to-maturation transition in mouse oocytes by sculpting the transcriptome to degrade RNAs encoding growth-phase factors and, thus, support the maturation phase of oogenesis.
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Affiliation(s)
- Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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Rahmani F, Rayzan E, Rahmani MR, Shahkarami S, Zoghi S, Rezaei A, Aryan Z, Najafi M, Rohlfs M, Jeske T, Aflatoonian M, Chavoshzadeh Z, Farahmand F, Motamed F, Rohani P, Alimadadi H, Mahdaviani A, Mansouri M, Tavakol M, Vanderberg M, Kotlarz D, Klein C, Rezaei N. Clinical and Mutation Description of the First Iranian Cohort of Infantile Inflammatory Bowel Disease: The Iranian Primary Immunodeficiency Registry (IPIDR). Immunol Invest 2020; 50:445-459. [PMID: 32633164 DOI: 10.1080/08820139.2020.1776725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We describe a cohort of 25 Iranian patients with infantile inflammatory bowel disease (IBD), 14 (56%) of whom had monogenic defects. After proper screening, patients were referred for whole exome sequencing (WES). Four patients had missense mutations in the IL10 RA, and one had a large deletion in the IL10 RB. Four patients had mutations in genes implicated in host:microbiome homeostasis, including TTC7A deficiency, and two patients with novel mutations in the TTC37 and NOX1. We found a novel homozygous mutation in the SRP54 in a deceased patient and the heterozygous variant in his sibling with a milder phenotype. Three patients had combined immunodeficiency: one with ZAP-70 deficiency (T+B+NK-), and two with atypical SCID due to mutations in RAG1 and LIG4. One patient had a G6PC3 mutation without neutropenia. Eleven of the 14 patients with monogenic defects were results of consanguinity and only 4 of them were alive to this date.
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Affiliation(s)
- Farzaneh Rahmani
- Department of Radiology, Washington University School of Medicine, St Louis, Missouri, USA.,Student's Scientific Research Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran.,NeuroImaging Network (NIN), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Elham Rayzan
- International Hematology/Oncology of Pediatrics' Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahmani
- Department of Immunology & Hematology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Sepideh Shahkarami
- Medical Genetics Network (Megene), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Arezoo Rezaei
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Aryan
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehri Najafi
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Meino Rohlfs
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Tim Jeske
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Majid Aflatoonian
- Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Pediatric Infectious Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Farahmand
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Motamed
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Pejman Rohani
- Pediatric Gastroenterology, Hepatology and Nutrition Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Alimadadi
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mahdaviani
- Pediatric Congenital Hematologic Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahboubeh Mansouri
- Immunology and Allergy Department, Mofid Children Hospital, Shahid Behehshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Tavakol
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mirjam Vanderberg
- Laboratory for Immunology, Dept. Of Pediatrics, Leiden University Medical Center, Netherlands
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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34
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Abstract
Primary antibody deficiencies (PADs) are the most common types of inherited primary immunodeficiency diseases (PIDs) presenting at any age, with a broad spectrum of clinical manifestations including susceptibility to infections, autoimmunity and cancer. Antibodies are produced by B cells, and consequently, genetic defects affecting B cell development, activation, differentiation or antibody secretion can all lead to PADs. Whole exome and whole genome sequencing approaches have helped identify genetic defects that are involved in the pathogenesis of PADs. Here, we summarize the clinical manifestations, causal genes, disease mechanisms and clinical treatments of different types of PADs.
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Melki I, Frémond ML. Type I Interferonopathies: from a Novel Concept to Targeted Therapeutics. Curr Rheumatol Rep 2020; 22:32. [DOI: 10.1007/s11926-020-00909-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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36
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Abstract
Early diagnosis of diarrhea is critical to prevent disease progression. Diarrhea in newborns can be congenital or acquired; acquired diarrheas are the major cause in infants. Congenital diarrheal diseases are rare and include defects in digestion, absorption, and transport of nutrients, and electrolytes; disorders of enterocyte differentiation and polarization; defects of enteroendocrine cell differentiation; dysregulation of the intestinal immune response; and dysfunction of the immune system. This review discusses the clinical approach that may help in early identification and management of different congenital diarrheal diseases.
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Affiliation(s)
- Mira Younis
- Department of Neonatology, Cleveland Clinic Children's, 9500 Euclid Avenue, M31-37, Cleveland, OH 44195, USA; Cleveland Clinic Lerner's College of Medicine, EC-10 Cleveland Clinic, 9501 Euclid Ave, Cleveland, OH 44195, USA
| | - Radhika Rastogi
- Cleveland Clinic Lerner's College of Medicine, EC-10 Cleveland Clinic, 9501 Euclid Ave, Cleveland, OH 44195, USA
| | - Ankur Chugh
- Pediatric Gastroenterology, Medical College of Wisconsin, 9000 W. Wisconsin Av, 6(th) Floor Clinics, Suite 610, Milwaukee, WI 53226, USA
| | - Shantanu Rastogi
- Newborn Services, George Washington University Hospital, Children's National Medical Center, 900 23rd Street, NW G2092, Washington, DC 20037, USA
| | - Hany Aly
- Department of Neonatology, Cleveland Clinic Children's, 9500 Euclid Avenue, M31-37, Cleveland, OH 44195, USA; Cleveland Clinic Lerner's College of Medicine, EC-10 Cleveland Clinic, 9501 Euclid Ave, Cleveland, OH 44195, USA.
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37
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van Son M, Tremoen NH, Gaustad AH, Våge DI, Zeremichael TT, Myromslien FD, Grindflek E. Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility. BMC Vet Res 2020; 16:161. [PMID: 32456687 PMCID: PMC7249385 DOI: 10.1186/s12917-020-02373-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sperm hyperactive motility has previously been shown to influence litter size in pigs, but little is known about the underlying biological mechanisms. The aim of this study was to use RNA sequencing to investigate gene expression differences in testis tissue from Landrace and Duroc boars with high and low levels of sperm hyperactive motility. Boars with divergent phenotypes were selected based on their sperm hyperactivity values at the day of ejaculation (day 0) (contrasts (i) and (ii) for Landrace and Duroc, respectively) and on their change in hyperactivity between day 0 and after 96 h liquid storage at 18 °C (contrast (iii)). RESULTS RNA sequencing was used to measure gene expression in testis. In Landrace boars, 3219 genes were differentially expressed for contrast (i), whereas 102 genes were differentially expressed for contrast (iii). Forty-one differentially expressed genes were identified in both contrasts, suggesting a functional role of these genes in hyperactivity regardless of storage. Zinc finger DNLZ was the most up-regulated gene in contrasts (i) and (iii), whereas the most significant differentially expressed gene for the two contrasts were ADP ribosylation factor ARFGAP1 and solute carrier SLC40A1, respectively. For Duroc (contrast (ii)), the clustering of boars based on their gene expression data did not reflect their difference in sperm hyperactivity phenotypes. No results were therefore obtained for this breed. A case-control analysis of variants identified in the Landrace RNA sequencing data showed that SNPs in NEU3, CHRDL2 and HMCN1 might be important for sperm hyperactivity. CONCLUSIONS Differentially expressed genes were identified in Landrace boars with high and low levels of sperm hyperactivity at the day of ejaculate collection and high and low change in hyperactivity after 96 h of sperm storage. The results point towards important candidate genes, biochemical pathways and sequence variants underlying sperm hyperactivity in pigs.
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Affiliation(s)
| | - Nina Hårdnes Tremoen
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Ann Helen Gaustad
- Norsvin SA, 2317 Hamar, Norway
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway
| | - Dag Inge Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway
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Ohnuma K, Kishita Y, Nyuzuki H, Kohda M, Ohtsu Y, Takeo S, Asano T, Sato-Miyata Y, Ohtake A, Murayama K, Okazaki Y, Aigaki T. Ski3/TTC37 deficiency associated with trichohepatoenteric syndrome causes mitochondrial dysfunction in Drosophila. FEBS Lett 2020; 594:2168-2181. [PMID: 32294252 DOI: 10.1002/1873-3468.13792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 11/08/2022]
Abstract
Tetratricopeptide repeat protein 37 (TTC37) is a causative gene of trichohepatoenteric syndrome (THES). However, little is known about the pathogenesis of this disease. Here, we characterize the phenotype of a Drosophila model in which ski3, a homolog of TTC37, is disrupted. The mutant flies are pupal lethal, and the pupal lethality is partially rescued by transgenic expression of wild-type ski3 or human TTC37. The mutant larvae show growth retardation, heart arrhythmia, triacylglycerol accumulation, and aberrant metabolism of glycolysis and the TCA cycle. Moreover, mitochondrial membrane potential and respiratory chain complex activities are significantly reduced in the mutants. Our results demonstrate that ski3 deficiency causes mitochondrial dysfunction, which may underlie the pathogenesis of THES.
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Affiliation(s)
- Kohei Ohnuma
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Yoshihito Kishita
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Japan
| | - Hiromi Nyuzuki
- Department of Pediatrics, School of Medicine, Niigata University, Asahimachi, Japan
| | - Masakazu Kohda
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Japan
| | - Yuta Ohtsu
- Division of Medical Nutrition, Faculty of Healthcare, Tokyo Healthcare University, Setagaya-ku, Japan
| | - Satomi Takeo
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Tsunaki Asano
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Yukiko Sato-Miyata
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
- Research and Education Centre for Natural Sciences, Keio University, Yokohama, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Saitama Medical University, Iruma-gun, Japan
| | - Kei Murayama
- Department of Metabolism, Center for Medical Genetics, Chiba Children's Hospital, Midori-ku, Japan
| | - Yasushi Okazaki
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Japan
| | - Toshiro Aigaki
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
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39
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Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell 2020; 77:1222-1236.e13. [PMID: 32048998 PMCID: PMC7083229 DOI: 10.1016/j.molcel.2020.01.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation.
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Affiliation(s)
- Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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40
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Kelsen JR, Sullivan KE, Rabizadeh S, Singh N, Snapper S, Elkadri A, Grossman AB. North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition Position Paper on the Evaluation and Management for Patients With Very Early-onset Inflammatory Bowel Disease. J Pediatr Gastroenterol Nutr 2020; 70:389-403. [PMID: 32079889 DOI: 10.1097/mpg.0000000000002567] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rate of pediatric inflammatory bowel disease (IBD) has been increasing over the last decade and this increase has occurred most rapidly in the youngest children diagnosed <6 years, known as very early-onset inflammatory bowel disease (VEO-IBD). These children can present with more extensive and severe disease than older children and adults. The contribution of host genetics in this population is underscored by the young age of onset and the distinct, aggressive phenotype. In fact, monogenic defects, often involving primary immunodeficiency genes, have been identified in children with VEO-IBD and have led to targeted and life-saving therapy. This position paper will discuss the phenotype of VEO-IBD and outline the approach and evaluation for these children and what factors should trigger concern for an underlying immunodeficiency. We will then review the immunological assays and genetic studies that can facilitate the identification of the underlying diagnosis in patients with VEO-IBD and how this evaluation may lead to directed therapies. The position paper will also aid the pediatric gastroenterologist in recognizing when a patient should be referred to a center specializing in the care of these patients. These guidelines are intended for pediatricians, allied health professionals caring for children, pediatric gastroenterologists, pediatric pathologists, and immunologists.
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Affiliation(s)
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shervin Rabizadeh
- Division of Gastroenterology, Hepatology, and Nutrition, Cedar-Sinai Medical Center, Los Angeles, CA
| | - Namita Singh
- Division of Gastroenterology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School
- Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Abdul Elkadri
- Division of Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI
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41
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Abstract
Congenital diarrheal disorders are heterogeneous conditions characterized by diarrhea with onset in the first years of life. They range from simple temporary conditions, such as cow's milk protein intolerance to irreversible complications, such as microvillous inclusion disease with significant morbidity and mortality. Advances in genomic medicine have improved our understanding of these disorders, leading to an ever-increasing list of identified causative genes. The diagnostic approach to these conditions consists of establishing the presence of diarrhea by detailed review of the history, followed by characterizing the composition of the diarrhea, the response to fasting, and with further specialized testing.
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Affiliation(s)
- Abdul Aziz Elkadri
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA.
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42
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Abstract
There are now 354 inborn errors of immunity (primary immunodeficiency diseases (PIDDs)) with 344 distinct molecular etiologies reported according to the International Union of Immunological Sciences (IUIS) (Clin Gastroenterol Hepatol 11: p. 1050-63, 2013, Semin Gastrointest Dis 8: p. 22-32, 1997, J Clin Immunol 38: p. 96-128, 2018). Using the IUIS document as a reference and cross-checking PubMed ( www.ncbi.nlm.nih.pubmed.gov ), we found that approximately one third of the 354 diseases of impaired immunity have a gastrointestinal component [J Clin Immunol 38: p. 96-128, 2018]. Often, the gastrointestinal symptomatology and pathology is the heralding sign of a PIDD; therefore, it is important to recognize patterns of disease which may manifest along the gastrointestinal tract as a more global derangement of immune function. As such, holistic consideration of immunity is warranted in patients with clinically significant gastrointestinal disease. Here, we discuss the manifold presentations and GI-specific complications of PIDDs which could lead patients to seek advice from a variety of clinician specialists. Often, patients with these medical problems will engage general pediatricians, surgeons, gastroenterologists, rheumatologists, and clinical immunologists among others. Following delineation of the presenting concern, accurate and often molecular diagnosis is imperative and a multi-disciplinary approach warranted for optimal management. In this review, we will summarize the current state of understanding of PIDD gastrointestinal disease involvement. We will do so by focusing upon gastrointestinal disease categories (i.e., inflammatory, diarrhea, nodular lymphoid hyperplasia, liver/biliary tract, structural disease, and oncologic disease) with an intent to aid the healthcare provider who may encounter a patient with an as-yet undiagnosed PIDD who presents initially with a gastrointestinal symptom, sign, or problem.
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43
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Abstract
The evolutionarily conserved RNA exosome is a multisubunit ribonuclease complex that processes and/or degrades numerous RNAs. Recently, mutations in genes encoding both structural and catalytic subunits of the RNA exosome have been linked to human disease. Mutations in the structural exosome gene EXOSC2 cause a distinct syndrome that includes retinitis pigmentosa, hearing loss, and mild intellectual disability. In contrast, mutations in the structural exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are related autosomal recessive, neurodegenerative diseases. In addition, mutations in the structural exosome gene EXOSC9 cause a PCH-like disease with cerebellar atrophy and spinal motor neuronopathy. Finally, mutations in the catalytic exosome gene DIS3 have been linked to multiple myeloma, a neoplasm of plasma B cells. How mutations in these RNA exosome genes lead to distinct, tissue-specific diseases is not currently well understood. In this chapter, we examine the role of the RNA exosome complex in human disease and discuss the mechanisms by which mutations in different exosome subunit genes could impair RNA exosome function and give rise to diverse diseases.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
| | - Derrick J Morton
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Emily G Kuiper
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephanie K Jones
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Sara W Leung
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Anita H Corbett
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
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Chang NW, Huang YP. The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis. Biomedicine (Taipei) 2019; 9:27. [PMID: 31724941 PMCID: PMC6855187 DOI: 10.1051/bmdcn/2019090427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Background: The activation of peroxisome proliferator-activated receptor alpha (PPARα) has been shown to reprogram tumor metabolism and exhibits great potential for treating anti-oral tumorigenesis. Methods: In this study, we used a pathway-based strategy to explore possible functional pathways involved in the anticancer activity of PPARα in oral cancer cells through next-generation sequencing (NGS) and bioinformatic approaches. Results: We found that 3919 genes were upregulated and 1060 genes were downregulated through PPARα activation. These genes were mainly involved in the proteasomal, mRNA surveillance, spliceosomal, RNA transport, and RNA degradation pathways, as indicated by GO and KEGG enrichment analysis. Importantly, a total of 13 upregulated genes in the RNA degradation pathway were identified including 3 core exosome factor genes (RRP43, RRP42, and CSL4), 2 TRAMP complex genes (TRF4 and Mtr4), 2 exosome cofactor genes (RRP6 and MPP6), 2 CCR4-NOT complex genes (CNOT2 and CNOT3), 2 Ski complex genes (SKI2 and Ski3), 1 decapping complex gene (EDC4), and 1 gene involved in 5’ exoribonuclease activity (XRN1). Conclusion: Our findings suggest that the activation of PPARα to upregulate the RNA degradation pathway might provide a new strategy for oral cancer treatment.
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Affiliation(s)
- Nai-Wen Chang
- Department of Biochemistry, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Yi-Ping Huang
- Department of Physiology, College of Medicine, China Medical University, Taichung 404, Taiwan
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45
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Aggarwal V, Banday AZ, Jindal AK, Das J, Rawat A. Recent advances in elucidating the genetics of common variable immunodeficiency. Genes Dis 2019; 7:26-37. [PMID: 32181273 PMCID: PMC7063417 DOI: 10.1016/j.gendis.2019.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/19/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Common variable immunodeficiency disorders (CVID), a heterogeneous group of inborn errors of immunity, is the most common symptomatic primary immunodeficiency disorder. Patients with CVID have highly variable clinical presentation. With the advent of whole genome sequencing and genome wide association studies (GWAS), there has been a remarkable improvement in understanding the genetics of CVID. This has also helped in understanding the pathogenesis of CVID and has drastically improved the management of these patients. A multi-omics approach integrating the DNA sequencing along with RNA sequencing, proteomics, epigenetic and metabolomics profile is the need of the hour to unravel specific CVID associated disease pathways and novel therapeutic targets. In this review, we elaborate various techniques that have helped in understanding the genetics of CVID.
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Affiliation(s)
- Vaishali Aggarwal
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aaqib Zaffar Banday
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ankur Kumar Jindal
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Jhumki Das
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Amit Rawat
- Allergy and Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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46
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Zhou D, Lai M, Luo A, Yu CY. An RNA Metabolism and Surveillance Quartet in the Major Histocompatibility Complex. Cells 2019; 8:E1008. [PMID: 31480283 PMCID: PMC6769589 DOI: 10.3390/cells8091008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
At the central region of the mammalian major histocompatibility complex (MHC) is a complement gene cluster that codes for constituents of complement C3 convertases (C2, factor B and C4). Complement activation drives the humoral effector functions for immune response. Sandwiched between the genes for serine proteinase factor B and anchor protein C4 are four less known but critically important genes coding for essential functions related to metabolism and surveillance of RNA during the transcriptional and translational processes of gene expression. These four genes are NELF-E (RD), SKIV2L (SKI2W), DXO (DOM3Z) and STK19 (RP1 or G11) and dubbed as NSDK. NELF-E is the subunit E of negative elongation factor responsible for promoter proximal pause of transcription. SKIV2L is the RNA helicase for cytoplasmic exosomes responsible for degradation of de-polyadenylated mRNA and viral RNA. DXO is a powerful enzyme with pyro-phosphohydrolase activity towards 5' triphosphorylated RNA, decapping and exoribonuclease activities of faulty nuclear RNA molecules. STK19 is a nuclear kinase that phosphorylates RNA-binding proteins during transcription. STK19 is also involved in DNA repair during active transcription and in nuclear signal transduction. The genetic, biochemical and functional properties for NSDK in the MHC largely stay as a secret for many immunologists. Here we briefly review the roles of (a) NELF-E on transcriptional pausing; (b) SKIV2L on turnover of deadenylated or expired RNA 3'→5' through the Ski-exosome complex, and modulation of inflammatory response initiated by retinoic acid-inducible gene 1-like receptor (RLR) sensing of viral infections; (c) DXO on quality control of RNA integrity through recognition of 5' caps and destruction of faulty adducts in 5'→3' fashion; and (d) STK19 on nuclear protein phosphorylations. There is compelling evidence that a dysregulation or a deficiency of a NSDK gene would cause a malignant, immunologic or digestive disease.
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Affiliation(s)
- Danlei Zhou
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.
| | - Michalea Lai
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
| | - Aiqin Luo
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Chack-Yung Yu
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA.
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47
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Poulton C, Pathak G, Mina K, Lassman T, Azmanov DN, McCormack E, Broley S, Dreyer L, Gration D, Taylor E, OSullivan M, Siafarikis A, Ravikumara M, Dawkins H, Pachter N, Baynam G. Tricho-hepatic-enteric syndrome (THES) without intractable diarrhoea. Gene 2019; 699:110-114. [PMID: 30844479 PMCID: PMC7872052 DOI: 10.1016/j.gene.2019.02.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/15/2023]
Abstract
Tricho-hepatic-enteric syndrome (THES) is a genetically heterogeneous rare syndrome (OMIM: 222470 (THES1) and 614602 (THES2)) that typically presents in the neonatal period with intractable diarrhoea, intra-uterine growth retardation (IUGR), facial dysmorphism, and hair and skin changes. THES is associated with pathogenic variants in either TTC37 or SKIV2L; both are components of the human SKI complex, an RNA exosome cofactor. We report an 8 year old girl who was diagnosed with THES by the Undiagnosed Disease Program-WA with compound heterozygous pathogenic variants in SKIV2L. While THES was considered in the differential diagnosis, the absence of protracted diarrhoea delayed definitive diagnosis. We therefore suggest that SKIV2L testing should be considered in cases otherwise suggestive of THES, but without the characteristic diarrhoea. We expand the phenotypic spectrum while reviewing the current knowledge on SKIV2L.
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Affiliation(s)
- C Poulton
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia.
| | - G Pathak
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - K Mina
- Douglass Hanly Moir Pathology, Macquarie Park, New South Wales, Australia
| | - T Lassman
- Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - D N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - E McCormack
- Faculty of Science, Doctor of Medicine Program, University of Western Australia, Perth, Western Australia, Australia
| | - S Broley
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia
| | - L Dreyer
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia
| | - D Gration
- Western Australia Register for Developmental Abnormalities, King Edward Memorial Hospital for Women Perth, Australia
| | - E Taylor
- Department of Paediatrics, Perth Children's Hospital Foundation, Nedlands, Australia
| | - M OSullivan
- Department of Immunology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - A Siafarikis
- Department of Endocrinology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - M Ravikumara
- Department of Gastroenterology, Perth Children's Hospital Foundation, Nedlands, Australia
| | - H Dawkins
- Centre for Population Health Research, Curtin University of Technology, Bentley, Australia
| | - N Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - G Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia; Undiagnosed Disease Program, Perth Children's Hospital Foundation, Nedlands, Australia; School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
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48
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Pazmandi J, Kalinichenko A, Ardy RC, Boztug K. Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. Immunol Rev 2019; 287:162-185. [PMID: 30565237 PMCID: PMC7379380 DOI: 10.1111/imr.12726] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
Rare, monogenetic diseases present unique models to dissect gene functions and biological pathways, concomitantly enhancing our understanding of the etiology of complex (and often more common) traits. Although inflammatory bowel disease (IBD) is a generally prototypic complex disease, it can also manifest in an early-onset, monogenic fashion, often following Mendelian modes of inheritance. Recent advances in genomic technologies have spurred the identification of genetic defects underlying rare, very early-onset IBD (VEO-IBD) as a disease subgroup driven by strong genetic influence, pinpointing key players in the delicate homeostasis of the immune system in the gut and illustrating the intimate relationships between bowel inflammation, systemic immune dysregulation, and primary immunodeficiency with increased susceptibility to infections. As for other human diseases, it is likely that adult-onset diseases may represent complex diseases integrating the effects of host genetic susceptibility and environmental triggers. Comparison of adult-onset IBD and VEO-IBD thus provides beautiful models to investigate the relationship between monogenic and multifactorial/polygenic diseases. This review discusses the present and novel findings regarding monogenic IBD as well as key questions and future directions of IBD research.
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Affiliation(s)
- Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Artem Kalinichenko
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Rico Chandra Ardy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Pediatrics and Adolescent MedicineMedical University of ViennaViennaAustria
- Department of PediatricsSt. Anna Kinderspital and Children's Cancer Research InstituteMedical University of ViennaViennaAustria
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49
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Gambineri E, Ciullini Mannurita S, Hagin D, Vignoli M, Anover-Sombke S, DeBoer S, Segundo GRS, Allenspach EJ, Favre C, Ochs HD, Torgerson TR. Clinical, Immunological, and Molecular Heterogeneity of 173 Patients With the Phenotype of Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked (IPEX) Syndrome. Front Immunol 2018; 9:2411. [PMID: 30443250 PMCID: PMC6223101 DOI: 10.3389/fimmu.2018.02411] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-linked (IPEX) Syndrome is a rare recessive disorder caused by mutations in the FOXP3 gene. In addition, there has been an increasing number of patients with wild-type FOXP3 gene and, in some cases, mutations in other immune regulatory genes. Objective: To molecularly asses a cohort of 173 patients with the IPEX phenotype and to delineate the relationship between the clinical/immunologic phenotypes and the genotypes. Methods: We reviewed the clinical presentation and laboratory characteristics of each patient and compared clinical and laboratory data of FOXP3 mutation-positive (IPEX patients) with those from FOXP3 mutation-negative patients (IPEX-like). A total of 173 affected patients underwent direct sequence analysis of the FOXP3 gene while 85 IPEX-like patients with normal FOXP3 were investigated by a multiplex panel of "Primary Immune Deficiency (PID-related) genes." Results: Forty-four distinct FOXP3 variants were identified in 88 IPEX patients, 9 of which were not previously reported. Among the 85 IPEX-like patients, 19 different disease-associated variants affecting 9 distinct genes were identified. Conclusions: We provide a comprehensive analysis of the clinical features and molecular bases of IPEX and IPEX-like patients. Although we were not able to identify major distinctive clinical features to differentiate IPEX from IPEX-like syndromes, we propose a simple flow-chart to effectively evaluate such patients and to focus on the most likely molecular diagnosis. Given the large number of potential candidate genes and overlapping phenotypes, selecting a panel of PID-related genes will facilitate a molecular diagnosis.
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Affiliation(s)
- Eleonora Gambineri
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - Sara Ciullini Mannurita
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - David Hagin
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Marina Vignoli
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | | | - Stacey DeBoer
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Gesmar R. S. Segundo
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Eric J. Allenspach
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Claudio Favre
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - Hans D. Ochs
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Troy R. Torgerson
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
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50
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Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A. A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans. Nucleic Acids Res 2018; 45:2068-2080. [PMID: 28204585 PMCID: PMC5389692 DOI: 10.1093/nar/gkw862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 12/18/2022] Open
Abstract
The exosome complex is a major eukaryotic exoribonuclease that requires the SKI complex for its activity in the cytoplasm. In yeast, the Ski7 protein links both complexes, whereas a functional equivalent of the Ski7 has remained unknown in the human genome. Proteomic analysis revealed that a previously uncharacterized short splicing isoform of HBS1L (HBS1LV3) is the long-sought factor linking the exosome and SKI complexes in humans. In contrast, the canonical HBS1L variant, HBS1LV1, which acts as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. Interestingly, both HBS1LV1 and HBS1LV3 interact with the SKI complex and HBS1LV1 seems to antagonize SKI/exosome supercomplex formation. HBS1LV3 contains a unique C-terminal region of unknown structure, with a conserved RxxxFxxxL motif responsible for exosome binding and may interact with the exosome core subunit RRP43 in a way that resembles the association between Rrp6 RNase and Rrp43 in yeast. HBS1LV3 or the SKI complex helicase (SKI2W) depletion similarly affected the transcriptome, deregulating multiple genes. Furthermore, half-lives of representative upregulated mRNAs were increased, supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway, essential for transcriptome homeostasis in the cytoplasm.
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Affiliation(s)
- Katarzyna Kalisiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz M. Kuliński
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zbigniew Pietras
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- To whom correspondence should be addressed. Tel: +48 22 5922033; Fax: +48 22 6584176;
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