1
|
Hale AT, Boudreau H, Devulapalli R, Duy PQ, Atchley TJ, Dewan MC, Goolam M, Fieggen G, Spader HL, Smith AA, Blount JP, Johnston JM, Rocque BG, Rozzelle CJ, Chong Z, Strahle JM, Schiff SJ, Kahle KT. The genetic basis of hydrocephalus: genes, pathways, mechanisms, and global impact. Fluids Barriers CNS 2024; 21:24. [PMID: 38439105 PMCID: PMC10913327 DOI: 10.1186/s12987-024-00513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
Hydrocephalus (HC) is a heterogenous disease characterized by alterations in cerebrospinal fluid (CSF) dynamics that may cause increased intracranial pressure. HC is a component of a wide array of genetic syndromes as well as a secondary consequence of brain injury (intraventricular hemorrhage (IVH), infection, etc.) that can present across the age spectrum, highlighting the phenotypic heterogeneity of the disease. Surgical treatments include ventricular shunting and endoscopic third ventriculostomy with or without choroid plexus cauterization, both of which are prone to failure, and no effective pharmacologic treatments for HC have been developed. Thus, there is an urgent need to understand the genetic architecture and molecular pathogenesis of HC. Without this knowledge, the development of preventive, diagnostic, and therapeutic measures is impeded. However, the genetics of HC is extraordinarily complex, based on studies of varying size, scope, and rigor. This review serves to provide a comprehensive overview of genes, pathways, mechanisms, and global impact of genetics contributing to all etiologies of HC in humans.
Collapse
Affiliation(s)
- Andrew T Hale
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK.
| | - Hunter Boudreau
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Rishi Devulapalli
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Phan Q Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Travis J Atchley
- Department of Neurosurgery, University of Alabama at Birmingham, FOT Suite 1060, 1720 2ndAve, Birmingham, AL, 35294, UK
| | - Michael C Dewan
- Division of Pediatric Neurosurgery, Monroe Carell Jr. Children's Hospital, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mubeen Goolam
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Graham Fieggen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Pediatric Neurosurgery, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - Heather L Spader
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Anastasia A Smith
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jeffrey P Blount
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - James M Johnston
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Brandon G Rocque
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Curtis J Rozzelle
- Division of Pediatric Neurosurgery, Children's of Alabama, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Zechen Chong
- Heflin Center for Genomics, University of Alabama at Birmingham, Birmingham, AL, UK
| | - Jennifer M Strahle
- Division of Pediatric Neurosurgery, St. Louis Children's Hospital, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Robinson CM, Duggan A, Forrester A. ER exit in physiology and disease. Front Mol Biosci 2024; 11:1352970. [PMID: 38314136 PMCID: PMC10835805 DOI: 10.3389/fmolb.2024.1352970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
The biosynthetic secretory pathway is comprised of multiple steps, modifications and interactions that form a highly precise pathway of protein trafficking and secretion, that is essential for eukaryotic life. The general outline of this pathway is understood, however the specific mechanisms are still unclear. In the last 15 years there have been vast advancements in technology that enable us to advance our understanding of this complex and subtle pathway. Therefore, based on the strong foundation of work performed over the last 40 years, we can now build another level of understanding, using the new technologies available. The biosynthetic secretory pathway is a high precision process, that involves a number of tightly regulated steps: Protein folding and quality control, cargo selection for Endoplasmic Reticulum (ER) exit, Golgi trafficking, sorting and secretion. When deregulated it causes severe diseases that here we categorise into three main groups of aberrant secretion: decreased, excess and altered secretion. Each of these categories disrupts organ homeostasis differently, effecting extracellular matrix composition, changing signalling events, or damaging the secretory cells due to aberrant intracellular accumulation of secretory proteins. Diseases of aberrant secretion are very common, but despite this, there are few effective therapies. Here we describe ER exit sites (ERES) as key hubs for regulation of the secretory pathway, protein quality control and an integratory hub for signalling within the cell. This review also describes the challenges that will be faced in developing effective therapies, due to the specificity required of potential drug candidates and the crucial need to respect the fine equilibrium of the pathway. The development of novel tools is moving forward, and we can also use these tools to build our understanding of the acute regulation of ERES and protein trafficking. Here we review ERES regulation in context as a therapeutic strategy.
Collapse
Affiliation(s)
- Claire M Robinson
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Aislinn Duggan
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Forrester
- Research Unit of Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
| |
Collapse
|
3
|
Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
Collapse
Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
| |
Collapse
|
4
|
Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
Collapse
Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | | |
Collapse
|
5
|
Takahashi Y, Date H, Oi H, Adachi T, Imanishi N, Kimura E, Takizawa H, Kosugi S, Matsumoto N, Kosaki K, Matsubara Y, Mizusawa H. Six years' accomplishment of the Initiative on Rare and Undiagnosed Diseases: nationwide project in Japan to discover causes, mechanisms, and cures. J Hum Genet 2022; 67:505-513. [PMID: 35318459 PMCID: PMC9402437 DOI: 10.1038/s10038-022-01025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 11/09/2022]
Abstract
The identification of causative genetic variants for hereditary diseases has revolutionized clinical medicine and an extensive collaborative framework with international cooperation has become a global trend to understand rare disorders. The Initiative on Rare and Undiagnosed Diseases (IRUD) was established in Japan to provide accurate diagnosis, discover causes, and ultimately provide cures for rare and undiagnosed diseases. The fundamental IRUD system consists of three pillars: IRUD diagnostic coordination, analysis centers (IRUD-ACs), and a data center (IRUD-DC). IRUD diagnostic coordination consists of clinical centers (IRUD-CLs) and clinical specialty subgroups (IRUD-CSSs). In addition, the IRUD coordinating center (IRUD-CC) manages the entire IRUD system and temporarily operates the IRUD resource center (IRUD-RC). By the end of March 2021, 6301 pedigrees consisting of 18,136 individuals were registered in the IRUD. The whole-exome sequencing method was completed in 5136 pedigrees, and a final diagnosis was established in 2247 pedigrees (43.8%). The total number of aberrated genes and pathogenic variants was 657 and 1718, among which 1113 (64.8%) were novel. In addition, 39 novel disease entities or phenotypes with 41 aberrated genes were identified. The 6-year endeavor of IRUD has been an overwhelming success, establishing an all-Japan comprehensive diagnostic and research system covering all geographic areas and clinical specialties/subspecialties. IRUD has accurately diagnosed diseases, identified novel aberrated genes or disease entities, discovered many candidate genes, and enriched phenotypic and pathogenic variant databases. Further promotion of the IRUD is essential for determining causes and developing cures for rare and undiagnosed diseases.
Collapse
Affiliation(s)
- Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hidetoshi Date
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hideki Oi
- Department of Clinical Data Science, Clinical Research and Education Promotion Division, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Takeya Adachi
- Keio Frontier Research & Education Collaborative Square (K-FRECS) at Tonomachi, Keio University, Kawasaki, Japan.,Department of Medical Regulatory Science, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Noriaki Imanishi
- Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.,Department of Research Promotion and Management, National Cerebral and Cardiovascular Center, Suita, Japan
| | - En Kimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.,Astellas Pharma Incorporated, Tokyo, Japan
| | - Hotake Takizawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Shinji Kosugi
- Department of Medical Ethics/Medical Genetics, Kyoto University School of Public Health, Kyoto, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | | | | | - Hidehiro Mizusawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.
| |
Collapse
|
6
|
Miao Y, Chen J, Guo X, Wei Y, Wu X, Sang Y, Wu D. Case report: Clinical manifestations and genotype analysis of a child with PTPN11 and SEC24D mutations. Front Pediatr 2022; 10:973920. [PMID: 36186652 PMCID: PMC9524269 DOI: 10.3389/fped.2022.973920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The PTPN11 gene, located at 12q24. 13, encodes protein tyrosine phosphatase 2C. Mutations in the PTPN11 gene can lead to various phenotypes, including Noonan syndrome and LEOPARD syndrome. The SEC24D gene is located at 4q26 and encodes a component of the COPII complex, and is closely related to endoplasmic reticulum protein transport. Mutations in SEC24D can lead to Cole-Carpenter syndrome-2. To date, dual mutations in these two genes have not been reported in the literature. METHODS We report a patient with short stature and osteogenesis imperfecta as the primary clinical manifestation. Other clinical features were peculiar facial features, deafness, and a history of recurrent fractures. Whole exome sequencing was performed on this patient. RESULTS After whole-exome sequencing, three mutations in two genes were identified that induced protein alterations associated with the patient's phenotype. One was a de novo variant c.1403C>T (p.Thr468Met) on exon 12 of the PTPN11 gene, and the other was a compound heterozygous mutation in the SEC24D gene, a novel variant c.2609_2610delGA (p.Arg870Thrfs*10) on exon 20 and a reported variant c.938G>A (p.Arg313His) on exon 8. CONCLUSIONS Concurrent mutations in PTPN11 and SEC24D induced a phenotype that was significantly different from individual mutations in either PTPN11 or SEC24D gene. Personalized genetic analysis and interpretation could help us understand the patient's etiology and hence develop treatments and improve the prognosis of these patients.
Collapse
Affiliation(s)
- Yuqi Miao
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jiahui Chen
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xiaoya Guo
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Yu Wei
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Xiaozhi Wu
- Beijing Haidian Hospital, Haidian Section of Peking University Third Hospital, Beijing, China
| | - Yanmei Sang
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Di Wu
- Department of Endocrinology, Genetics and Metabolism, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, Beijing, China
| |
Collapse
|
7
|
Lu CL, Kim J. Craniofacial Diseases Caused by Defects in Intracellular Trafficking. Genes (Basel) 2021; 12:726. [PMID: 34068038 PMCID: PMC8152478 DOI: 10.3390/genes12050726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Cells use membrane-bound carriers to transport cargo molecules like membrane proteins and soluble proteins, to their destinations. Many signaling receptors and ligands are synthesized in the endoplasmic reticulum and are transported to their destinations through intracellular trafficking pathways. Some of the signaling molecules play a critical role in craniofacial morphogenesis. Not surprisingly, variants in the genes encoding intracellular trafficking machinery can cause craniofacial diseases. Despite the fundamental importance of the trafficking pathways in craniofacial morphogenesis, relatively less emphasis is placed on this topic, thus far. Here, we describe craniofacial diseases caused by lesions in the intracellular trafficking machinery and possible treatment strategies for such diseases.
Collapse
Affiliation(s)
| | - Jinoh Kim
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| |
Collapse
|
8
|
Higuchi Y, Hasegawa K, Futagawa N, Yamashita M, Tanaka H, Tsukahara H. Genetic analysis in Japanese patients with osteogenesis imperfecta: Genotype and phenotype spectra in 96 probands. Mol Genet Genomic Med 2021; 9:e1675. [PMID: 33939306 PMCID: PMC8222851 DOI: 10.1002/mgg3.1675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/14/2021] [Accepted: 03/23/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Osteogenesis imperfecta (OI) is a rare connective-tissue disorder characterized by bone fragility. Approximately 90% of all OI cases are caused by variants in COL1A1 or COL1A2. Additionally, IFITM5 variants are responsible for the unique OI type 5. We previously analyzed COL1A1/2 variants in 22 Japanese families with OI through denaturing high-performance liquid chromatography screening, but our detection rate was low (41%). METHODS To expand the genotype-phenotype correlations, we performed a genetic analysis of COL1A1/2 and IFITM5 in 96 non-consanguineous Japanese OI probands by Sanger sequencing. RESULTS Of these individuals, 54, 41, and 1 had type 1 (mild), type 2-4 (moderate-to-severe), and type 5 phenotypes, respectively. In the mild group, COL1A1 nonsense and splice-site variants were prevalent (n = 30 and 20, respectively), but there were also COL1A1 and COL1A2 triple-helical glycine substitutions (n = 2 and 1, respectively). In the moderate-to-severe group, although COL1A1 and COL1A2 glycine substitutions were common (n = 14 and 18, respectively), other variants were also detected. The single case of type 5 had the characteristic c.-14C>T variant in IFITM5. CONCLUSION These results increase our previous detection rate for COL1A1/2 variants to 99% and provide insight into the genotype-phenotype correlations in OI.
Collapse
Affiliation(s)
- Yousuke Higuchi
- Department of Pediatrics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kosei Hasegawa
- Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Natsuko Futagawa
- Department of Pediatrics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.,Department of Pediatrics, Okayama University Hospital, Okayama, Japan
| | - Miho Yamashita
- Faculty of Human Life Sciences, Notre Dame Seishin University, Okayama, Japan
| | - Hiroyuki Tanaka
- Department of Pediatrics, Okayama Saiseikai General Hospital, Okayama, Japan
| | - Hirokazu Tsukahara
- Department of Pediatrics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| |
Collapse
|
9
|
Omari S, Makareeva E, Gorrell L, Jarnik M, Lippincott-Schwartz J, Leikin S. Mechanisms of procollagen and HSP47 sorting during ER-to-Golgi trafficking. Matrix Biol 2020; 93:79-94. [DOI: 10.1016/j.matbio.2020.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/27/2022]
|
10
|
Chen TY, Liu Y, Chen L, Luo J, Zhang C, Shen XF. Identification of the potential biomarkers in patients with glioma: a weighted gene co-expression network analysis. Carcinogenesis 2020; 41:743-750. [PMID: 31761927 PMCID: PMC7351128 DOI: 10.1093/carcin/bgz194] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/13/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
Glioma is the most common brain tumor with high mortality. However, there are still challenges for the timely and accurate diagnosis and effective treatment of the tumor. One hundred and twenty-one samples with grades II, III and IV from the Gene Expression Omnibus database were used to construct gene co-expression networks to identify hub modules closely related to glioma grade, and performed pathway enrichment analysis on genes from significant modules. In gene co-expression network constructed by 2345 differentially expressed genes from 121 gene expression profiles for glioma, we identified the black and blue modules that associated with grading. The module preservation analysis based on 118 samples indicates that the two modules were replicable. Enrichment analysis showed that the extracellular matrix genes were enriched for blue module, while cell division genes were enriched for black module. According to survival analysis, 21 hub genes were significantly up-regulated and one gene was significantly down-regulated. What’s more, IKBIP, SEC24D, and FAM46A are the genes with little attention among the 22 hub genes. In this study, IKBIP, SEC24D, and FAM46A related to glioma were mentioned for the first time to the current knowledge, which might provide a new idea for us to study the disease in the future. IKBIP, SEC24D and FAM46A among the 22 hub genes identified that are related to the malignancy degree of glioma might be used as new biomarkers to improve the diagnosis, treatment and prognosis of glioma.
Collapse
Affiliation(s)
- Ting-Yu Chen
- Center for Evidence-Based Medicine and Clinical Research, Shiyan, China
| | - Yang Liu
- Center for Evidence-Based Medicine and Clinical Research, Shiyan, China
| | - Liang Chen
- Department of Neurosurgery, Shiyan, China
| | - Jie Luo
- Center for Evidence-Based Medicine and Clinical Research, Shiyan, China.,Department of Neurosurgery, Shiyan, China
| | - Chao Zhang
- Center for Evidence-Based Medicine and Clinical Research, Shiyan, China
| | - Xian-Feng Shen
- Center for Evidence-Based Medicine and Clinical Research, Shiyan, China.,Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| |
Collapse
|