1
|
FMR1 mRNA from full mutation alleles is associated with ABC-C FX scores in males with fragile X syndrome. Sci Rep 2020; 10:11701. [PMID: 32678152 PMCID: PMC7367290 DOI: 10.1038/s41598-020-68465-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 02/08/2023] Open
Abstract
Fragile X syndrome (FXS) is caused by a hypermethylated full mutation (FM) expansion with ≥ 200 CGG repeats, and a decrease in FMR1 mRNA and its protein. However, incomplete silencing from FM alleles has been associated with more severe autism features in FXS males. This study compared scores on the Aberrant Behavior Checklist-Community-FXS version (ABC-CFX) in 62 males affected with FXS (3 to 32 years) stratified based on presence or absence of mosaicism and/or FMR1 mRNA silencing. Associations between ABC-CFX subscales and FMR1 mRNA levels, assessed using real-time PCR relative standard curve method, were also examined. The FXS group mosaic for premutation (PM: 55–199 CGGs) and FM alleles had lower irritability (p = 0.014) and inappropriate speech (p < 0.001) scores compared to males with only FM alleles and complete loss of FMR1 mRNA. The PM/FM mosaic group also showed lower inappropriate speech scores compared to the incomplete silencing (p = 0.002) group. Increased FMR1 mRNA levels were associated with greater irritability (p < 0.001), and lower health-related quality of life scores (p = 0.004), but only in the incomplete silencing FM-only group. The findings suggest that stratification based on CGG sizing and FMR1 mRNA levels may be warranted in future research and clinical trials utilising ABC-CFX subscales as outcome measures.
Collapse
|
2
|
Significantly Elevated FMR1 mRNA and Mosaicism for Methylated Premutation and Full Mutation Alleles in Two Brothers with Autism Features Referred for Fragile X Testing. Int J Mol Sci 2019; 20:ijms20163907. [PMID: 31405222 PMCID: PMC6721168 DOI: 10.3390/ijms20163907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 11/26/2022] Open
Abstract
Although fragile X syndrome (FXS) is caused by a hypermethylated full mutation (FM) expansion with ≥200 cytosine-guanine-guanine (CGG) repeats, and a decrease in FMR1 mRNA and its protein (FMRP), incomplete silencing has been associated with more severe autism features in FXS males. This study reports on brothers (B1 and B2), aged 5 and 2 years, with autistic features and language delay, but a higher non-verbal IQ in comparison to typical FXS. CGG sizing using AmplideX PCR only identified premutation (PM: 55–199 CGGs) alleles in blood. Similarly, follow-up in B1 only revealed PM alleles in saliva and skin fibroblasts; whereas, an FM expansion was detected in both saliva and buccal DNA of B2. While Southern blot analysis of blood detected an unmethylated FM, methylation analysis with a more sensitive methodology showed that B1 had partially methylated PM alleles in blood and fibroblasts, which were completely unmethylated in buccal and saliva cells. In contrast, B2 was partially methylated in all tested tissues. Moreover, both brothers had FMR1 mRNA ~5 fold higher values than those of controls, FXS and PM cohorts. In conclusion, the presence of unmethylated FM and/or PM in both brothers may lead to an overexpression of toxic expanded mRNA in some cells, which may contribute to neurodevelopmental problems, including elevated autism features.
Collapse
|
3
|
Baker EK, Arpone M, Aliaga SM, Bretherton L, Kraan CM, Bui M, Slater HR, Ling L, Francis D, Hunter MF, Elliott J, Rogers C, Field M, Cohen J, Cornish K, Santa Maria L, Faundes V, Curotto B, Morales P, Trigo C, Salas I, Alliende AM, Amor DJ, Godler DE. Incomplete silencing of full mutation alleles in males with fragile X syndrome is associated with autistic features. Mol Autism 2019; 10:21. [PMID: 31073396 PMCID: PMC6499941 DOI: 10.1186/s13229-019-0271-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background Fragile X syndrome (FXS) is a common monogenic cause of intellectual disability with autism features. While it is caused by loss of the FMR1 product (FMRP), mosaicism for active and inactive FMR1 alleles, including alleles termed premutation (PM: 55-199 CGGs), is not uncommon. Importantly, both PM and active full mutation (FM: ≥ 200 CGGs) alleles often express elevated levels of mRNA that are thought to be toxic. This study determined if complete FMR1 mRNA silencing from FM alleles and/or levels of FMR1 mRNA (if present) in blood are associated with intellectual functioning and autism features in FXS. Methods The study cohort included 98 participants (70.4% male) with FXS (FM-only and PM/FM mosaic) aged 1-43 years. A control group of 14 females were used to establish control FMR1 mRNA reference range. Intellectual functioning and autism features were assessed using the Mullen Scales of Early Learning or an age-appropriate Wechsler Scale and the Autism Diagnostic Observation Schedule-2nd Edition (ADOS-2), respectively. FMR1 mRNA was analysed in venous blood collected at the time of assessments, using the real-time PCR relative standard curve method. Results Females with FXS had significantly higher levels of FMR1 mRNA (p < 0.001) than males. FMR1 mRNA levels were positively associated with age (p < 0.001), but not with intellectual functioning and autistic features in females. FM-only males (aged < 19 years) expressing FM FMR1 mRNA had significantly higher ADOS calibrated severity scores compared to FM-only males with completely silenced FMR1 (p = 0.011). However, there were no significant differences between these subgroups on intellectual functioning. In contrast, decreased levels of FMR1 mRNA were associated with decreased intellectual functioning in FXS males (p = 0.029), but not autism features, when combined with the PM/FM mosaic group. Conclusion Incomplete silencing of toxic FM RNA may be associated with autistic features, but not intellectual functioning in FXS males. While decreased levels of mRNA may be more predictive of intellectual functioning than autism features. If confirmed in future studies, these findings may have implications for patient stratification, outcome measure development, and design of clinical and pre-clinical trials in FXS.
Collapse
Affiliation(s)
- Emma K. Baker
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Marta Arpone
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Brain and Mind, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Solange M. Aliaga
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
| | - Lesley Bretherton
- Brain and Mind, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Claudine M. Kraan
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Carlton, Australia
| | - Howard R. Slater
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
| | - Ling Ling
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
| | - David Francis
- Victorian Clinical Genetics Services and Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC Australia
| | - Matthew F. Hunter
- Monash Genetics, Monash Health, Melbourne, VIC Australia
- Department of Paediatrics, Monash University, Clayton, VIC Australia
| | - Justine Elliott
- Victorian Clinical Genetics Services and Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC Australia
| | - Carolyn Rogers
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW Australia
| | - Jonathan Cohen
- Fragile X Alliance Inc, North Caulfield, VIC and Center for Developmental Disability Health Victoria, Monash University, Clayton, Australia
| | - Kim Cornish
- Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Clayton, VIC Australia
| | - Lorena Santa Maria
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Victor Faundes
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Bianca Curotto
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Paulina Morales
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Cesar Trigo
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Isabel Salas
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - Angelica M. Alliende
- Molecular and Cytogenetics Laboratory, INTA, University of Chile, Santiago, Chile
| | - David J. Amor
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
- Neurodisability and Rehabilitation, Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - David E. Godler
- Diagnosis and Development, Murdoch Children’s Research Institute, Royal Children’s Hospital, 50 Flemington Rd, Parkville, VIC 3052 Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Australia
| |
Collapse
|
4
|
β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies. PLoS One 2018; 13:e0192151. [PMID: 29474364 PMCID: PMC5825026 DOI: 10.1371/journal.pone.0192151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/17/2018] [Indexed: 12/02/2022] Open
Abstract
Relationships between Fragile X Mental Retardation 1 (FMR1) mRNA levels in blood and intragenic FMR1 CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55–199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised FMR1 mRNA level to a single internal control gene called β-glucuronidase (GUS). This study evaluated FMR1 mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i) GUS as a single internal control; (ii) the mean of GUS, Eukaryotic Translation Initiation Factor 4A2 (EIF4A2) and succinate dehydrogenase complex flavoprotein subunit A (SDHA); and (iii) the mean of EIF4A2 and SDHA (with no contribution from GUS). GUS mRNA levels normalised to the mean of EIF4A2 and SDHA mRNA levels and EIF4A2/SDHA ratio were also evaluated. FMR1mRNA level normalised to the mean of EIF4A2 and SDHA mRNA levels, with no contribution from GUS, showed the most significant correlation with CGG size and the greatest difference between PM and control groups (p = 10−11). Only 15% of FMR1 mRNA PM results exceeded the maximum control value when normalised to GUS, compared with over 42% when normalised to the mean of EIF4A2 and SDHA mRNA levels. Neither GUS mRNA level normalised to the mean RNA levels of EIF4A2 and SDHA, nor to the EIF4A2/SDHA ratio were correlated with CGG size. However, greater variability in GUS mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the EIF4A2/SDHA ratio. In conclusion, normalisation with multiple control genes, excluding GUS, can improve assessment of the biological significance of FMR1 mRNA-CGG size relationships.
Collapse
|
5
|
Kraan CM, Cornish KM, Bui QM, Li X, Slater HR, Godler DE. β-glucuronidase mRNA levels are correlated with gait and working memory in premutation females: understanding the role of FMR1 premutation alleles. Sci Rep 2016; 6:29366. [PMID: 27387142 PMCID: PMC4937393 DOI: 10.1038/srep29366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/17/2016] [Indexed: 12/28/2022] Open
Abstract
Fragile X tremor ataxia syndrome (FXTAS) is a late-onset disorder manifesting in a proportion of FMR1 premutation individuals (PM: 55-199 CGG triplet expansions). FXTAS is associated with elevated levels of FMR1 mRNA which are toxic. In this study, relationships between neurocognitive and intra-step gait variability measures with mRNA levels, measured in blood samples, were examined in 35 PM and 35 matched control females. The real-time PCR assays measured FMR1 mRNA, and previously used internal control genes: β-Glucuronidase (GUS), Succinate Dehydrogenase 1 (SDHA) and Eukaryotic Translation Initiation Factor 4A (EI4A2). Although there was significant correlation of gait variability with FMR1 mRNA levels (p = 0.004) when normalized to GUS (FMR1/GUS), this was lost when FMR1 was normalized to SDHA and EI4A2 (2IC). In contrast, GUS mRNA level normalized to 2IC showed a strong correlation with gait variability measures (p < 0.007), working memory (p = 0.001) and verbal intelligence scores (p = 0.008). PM specific changes in GUS mRNA were not mediated by FMR1 mRNA. These results raise interest in the role of GUS in PM related disorders and emphasise the importance of using appropriate internal control genes, which have no significant association with PM phenotype, to normalize FMR1 mRNA levels.
Collapse
Affiliation(s)
- C M Kraan
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Clayton, Victoria, 3800, Australia
| | - K M Cornish
- School of Psychological Sciences and Monash Institute of Cognitive and Clinical Neurosciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Q M Bui
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne Carlton, Victoria, 3053, Australia
| | - X Li
- Cyto-molecular Diagnostic Research Laboratory, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia
| | - H R Slater
- Cyto-molecular Diagnostic Research Laboratory, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - D E Godler
- Cyto-molecular Diagnostic Research Laboratory, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria, 3052, Australia
| |
Collapse
|
6
|
Hocking DR, Kraan CM, Godler DE, Bui QM, Li X, Bradshaw JL, Georgiou-Karistianis N, Metcalfe SA, Archibald AD, Turbitt E, Fielding J, Trollor J, Cohen J, Cornish KM. Evidence linking FMR1 mRNA and attentional demands of stepping and postural control in women with the premutation. Neurobiol Aging 2014; 36:1400-8. [PMID: 25541421 DOI: 10.1016/j.neurobiolaging.2014.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/25/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
Recent studies in young adult females with the fragile X mental retardation 1 (FMR1) gene premutation (PM) have shown subtle but significant impairments in executive control and postural stability. Less is known about the influence of age and FMR1 gene expression on executive control and postural stability in females with the PM. Here, we examined the attentional demands of reactive stepping using a well-validated measure of choice stepping reaction time under dual-task interference. We explored the interrelationships between step initiation times during a concurrent verbal fluency task and specific impairments in executive control previously reported in females with the PM. Our results showed increased dual-task interference on step initiation times and variability in female PM compared with control subjects. In addition, we observed greater choice stepping reaction time dual-task costs above the breakpoint of 81 CGG repeats relative to below this CGG range. Dual-task interference on both reaction time and movement time were significantly predicted by low working memory capacity in female PM carriers. Importantly, we revealed that FMR1 messenger RNA level is the most significant predictor accounting for dual-task stepping variability in both reaction time and movement time in PM females. These findings for the first time provide evidence linking elevated FMR1 messenger RNA levels that have been previously associated with FMR1 RNA toxicity and deficits in cerebellar motor and cognitive networks in a subgroup of at-risk PM women.
Collapse
Affiliation(s)
- Darren R Hocking
- Olga Tennison Autism Research Centre, School of Psychological Science, La Trobe University, Bundoora, Victoria, Australia.
| | - Claudine M Kraan
- School of Psychological Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - David E Godler
- Cyto-molecular Diagnostics Research, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Quang M Bui
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Carlton, Victoria, Australia
| | - Xin Li
- Cyto-molecular Diagnostics Research, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - John L Bradshaw
- School of Psychological Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Nellie Georgiou-Karistianis
- School of Psychological Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sylvia A Metcalfe
- Genetics Education and Health Research, Murdoch Childrens Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Alison D Archibald
- Genetics Education and Health Research, Murdoch Childrens Research Institute, Parkville, Victoria, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Parkville, Victoria, Australia
| | - Erin Turbitt
- Genetics Education and Health Research, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Joanne Fielding
- School of Psychological Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Julian Trollor
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, Sydney, Australia; Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Jonathan Cohen
- Genetics Education and Health Research, Murdoch Childrens Research Institute, Parkville, Victoria, Australia; Centre for Developmental Disability Health Victoria, Monash University, Clayton, Victoria, Australia; Fragile X Alliance Inc (Clinic and Resource Centre), North Caulfield, Victoria, Australia
| | - Kim M Cornish
- School of Psychological Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
7
|
Slagter-Jäger JG, Raney A, Lewis WE, DeBenedette MA, Nicolette CA, Tcherepanova IY. Evaluation of RNA Amplification Methods to Improve DC Immunotherapy Antigen Presentation and Immune Response. MOLECULAR THERAPY. NUCLEIC ACIDS 2013; 2:e91. [PMID: 23653155 PMCID: PMC4817939 DOI: 10.1038/mtna.2013.18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 03/19/2013] [Indexed: 01/07/2023]
Abstract
Dendritic cells (DCs) transfected with total amplified tumor cell RNA have the potential to induce broad antitumor immune responses. However, analytical methods required for quantitatively assessing the integrity, fidelity, and functionality of the amplified RNA are lacking. We have developed a series of assays including gel electrophoresis, northern blot, capping efficiency, and microarray analysis to determine integrity and fidelity and a model system to assess functionality after transfection into human DCs. We employed these tools to demonstrate that modifications to our previously reported total cellular RNA amplification process including the use of the Fast Start High Fidelity (FSHF) PCR enzyme, T7 Powerswitch primer, post-transcriptional capping and incorporation of a type 1 cap result in amplification of longer transcripts, greater translational competence, and a higher fidelity representation of the starting total RNA population. To study the properties of amplified RNA after transfection into human DCs, we measured protein expression levels of defined antigens coamplified with the starting total RNA populations and measured antigen-specific T cell expansion in autologous DC-T cell co-cultured in vitro. We conclude from these analyses that the improved RNA amplification process results in superior protein expression levels and a greater capacity of the transfected DCs to induce multifunctional antigen-specific memory T cells.Molecular Therapy-Nucleic Acids (2013) 2, e91; doi:10.1038/mtna.2013.18; published online 7 May 2013.
Collapse
Affiliation(s)
| | - Alexa Raney
- Novartis, Holly Springs, North Carolina, USA
| | | | | | | | | |
Collapse
|
8
|
Slagter-Jäger JG, Nicolette CA, Tcherepanova IY. Evaluation of a microfluidics-based platform and slab electrophoresis for determination of size, integrity and quantification of in vitro transcribed RNA used as a component in therapeutic drug manufacturing. J Pharm Biomed Anal 2012; 70:657-63. [PMID: 22703839 DOI: 10.1016/j.jpba.2012.04.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/27/2012] [Accepted: 04/24/2012] [Indexed: 11/19/2022]
Abstract
Ribonucleic acid (RNA) is gaining utility as a key component of immunotherapeutics to transiently express antigens or to modulate endogenous gene expression for clinical applications. As a key ancillary component of clinical grade products, RNA requires a robust method for quality control. Here we evaluated the microfluidics based platform and slab electrophoresis for determination of integrity, concentration and size of four in vitro-transcribed RNA products with sizes of 1611, 808, 475 and 290 nucleotides (nts). Our data demonstrate that the Bioanalyzer can determine both size and integrity of the RNA, but the analysis suffers from a strong well position effect. For the RNAs tested, the integrity values obtained by the Bioanalyzer demonstrate a reverse correlation with the size of the molecule and are lower than those obtained using slab electrophoresis. Agarose gel electrophoresis produced the information on size of the RNA molecule with good precision, accuracy and reproducibility. We highlight observations which need to be taken into account when developing and qualifying a method of choice for assessment of in vitro-transcribed RNA using either approach.
Collapse
|
9
|
Evidence for the toxicity of bidirectional transcripts and mitochondrial dysfunction in blood associated with small CGG expansions in the FMR1 gene in patients with parkinsonism. Genet Med 2011; 13:392-9. [PMID: 21270637 DOI: 10.1097/gim.0b013e3182064362] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Our previous results showed that both gray zone and lower end premutation range (40-85 repeats) fragile X mental retardation 1 (FMR1) alleles were more common among males with parkinsonism than in the general population. This study aimed to determine whether these alleles have a significant role in the manifestations and pathogenesis of parkinsonian disorders. METHODS Detailed clinical assessment and genetic testing were performed in 14 male carriers of premutation and gray zone FMR1 alleles and in 24 noncarriers identified in a sample of males with parkinsonism. RESULTS The premutation + gray zone carriers presented with more severe symptoms than disease controls matched for age, diagnosis, disease duration, and treatment. The Parkinson disease (Unified Parkinson's Disease Rating Scale) motor score and the measures of cognitive decline (Mini-Mental State Examination and/or Addenbrooke's Cognitive Examination Final Revised Version A scores) were significantly correlated with the size of the CGG repeat and the (elevated) levels of antisense FMR1 and Cytochrome C1 mRNAs in blood leukocytes. In addition, the carriers showed a significant depletion of the nicotinamide adenine dinucleotide, reduced dehydrogenase subunit 1 mitochondrial gene in whole blood. CONCLUSION Small CGG expansion FMR1 alleles (gray zone and lower end premutation) play a significant role in the development of the parkinsonian phenotype, possibly through the cytotoxic effect of elevated sense and/or antisense FMR1 transcripts involving mitochondrial dysfunction and leading to progressive neurodegeneration.
Collapse
|
10
|
Wang EH, Truong LD, Mendoza L, Jung ES, Choi YJ. 28S-ribosomal RNA is superior to glyceraldehyde-3-phosphate dehydrogenase as a RNA reference gene in p53-deficient mice with unilateral ureteral obstruction. Exp Mol Pathol 2011; 91:368-72. [PMID: 21565186 DOI: 10.1016/j.yexmp.2011.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/19/2011] [Indexed: 11/30/2022]
Abstract
Although there are many kinds of reference genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been commonly used by many researchers to assess the amount and integrity of RNA transcripts in RNA studies including Northern blot and reverse transcription real time-PCR. Although some data suggest that GAPDH could be inconstant in their situations or experiments, there is limited evidence that GAPDH expression is influenced by conditions of experiment, especially in mouse kidney model with unilateral ureteral obstruction (UUO). Therefore, the establishment of excellent reference gene according to the tissue types or conditions of experiment is a bottom line for the RNA study. Here we compared the expression of GAPDH with 28S rRNA gene by Northern blot analysis in the p53-deficient mice with UUO. We observed that GAPDH mRNA levels in ligated kidneys were significantly lower than those in contralateral kidneys, especially after postoperative day 15. In contrast, 28S rRNA levels were constant among control, ligated and contralateral kidneys. We also demonstrated that 28S rRNA signal was proportional to the amount of RNA loaded. In conclusion, these data indicate that much caution should be taken when using GAPDH as a RNA reference gene and 28S rRNA is an excellent gene for the RNA study in p53-deficient mice with UUO.
Collapse
Affiliation(s)
- Eun-Hui Wang
- Department of Hospital Pathology, The Catholic University of Korea, Seocho-Gu, Seoul, Republic of Korea
| | | | | | | | | |
Collapse
|
11
|
Godler DE, Tassone F, Loesch DZ, Taylor AK, Gehling F, Hagerman RJ, Burgess T, Ganesamoorthy D, Hennerich D, Gordon L, Evans A, Choo KH, Slater HR. Methylation of novel markers of fragile X alleles is inversely correlated with FMRP expression and FMR1 activation ratio. Hum Mol Genet 2010; 19:1618-32. [PMID: 20118148 DOI: 10.1093/hmg/ddq037] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The fragile X syndrome (FXS) is caused by silencing of the fragile X mental retardation gene (FMR1) and the absence of its product, fragile X mental retardation protein (FMRP), resulting from CpG island methylation associated with large CGG repeat expansions (more than 200) termed full mutation (FM). We have identified a number of novel epigenetic markers for FXS using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), naming the most informative fragile X-related epigenetic element 1 (FREE1) and 2 (FREE2). Methylation of both regions was correlated with that of the FMR1 CpG island detected using Southern blot (FREE1 R = 0.97; P < 0.00001, n = 23 and FREE2 R = 0.93; P < 0.00001, n = 23) and negatively correlated with lymphocyte expression of FMRP (FREE1 R = -0.62; P = 0.01, n = 15 and FREE2 R = -0.55; P = 0.03, n = 15) in blood of partially methylated 'high functioning' FM males. In blood of FM carrier females, methylation of both markers was inversely correlated with the FMR1 activation ratio (FREE1 R = -0.93; P < 0.0001, n = 12 and FREE2 R = -0.95; P < 0.0001, n = 9). In a sample set of 49 controls, 18 grey zone (GZ 40-54 repeats), 22 premutation (PM 55-170 repeats) and 22 (affected) FXS subjects, the FREE1 methylation pattern was consistent between blood and chorionic villi as a marker of methylated FM alleles and could be used to differentiate FXS males and females from controls, as well as from carriers of GZ/PM alleles, but not between GZ and PM alleles and controls. Considering its high-throughput and specificity for pathogenic FM alleles, low cost and minimal DNA requirements, FREE MALDI-TOF MS offers a unique tool in FXS diagnostics and newborn population screening.
Collapse
Affiliation(s)
- David Eugeny Godler
- Chromosome and Chromatin Research Laboratory, The Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Loesch DZ, Godler DE, Khaniani M, Gould E, Gehling F, Dissanayake C, Burgess T, Tassone F, Huggins R, Slater H, Choo KHA. Linking the FMR1 alleles with small CGG expansions with neurodevelopmental disorders: preliminary data suggest an involvement of epigenetic mechanisms. Am J Med Genet A 2009; 149A:2306-10. [PMID: 19760650 DOI: 10.1002/ajmg.a.32990] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Danuta Z Loesch
- The Olga Tennison Centre for Autism Research, School of Psychological Science, La Trobe University, Melbourne, Victoria, Australia.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|