26
|
O'Neill DG, Mitchell CE, Humphrey J, Church DB, Brodbelt DC, Pegram C. Epidemiology of periodontal disease in dogs in the UK primary-care veterinary setting. J Small Anim Pract 2021; 62:1051-1061. [PMID: 34374104 PMCID: PMC9291557 DOI: 10.1111/jsap.13405] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/01/2021] [Accepted: 07/15/2021] [Indexed: 11/26/2022]
Abstract
Objectives Periodontal disease is a frequent diagnosis of dogs and can have severe negative impacts on welfare. It was hypothesised that breeds with skull shapes that differ most in conformation from the moderate mesocephalic skull shape have higher odds of periodontal disease. Materials and Methods The cohort study included a random sample of dogs under primary veterinary care in 2016 from the VetCompass Programme database. Risk factor analysis used random effects multivariable logistic regression modelling. Results The study included a random sample of 22,333 dogs. The 1‐year period prevalence for diagnosis with periodontal disease was 12.52% (95% CI: 12.09 to 12.97). Eighteen breeds showed increased odds compared with crossbred dogs. Breeds with the highest odds included Toy Poodle (odds ratio 3.97, 95% confidence intervals 2.21 to 7.13), King Charles Spaniel (odds ratio 2.63, 95% confidence interval 1.50 to 4.61), Greyhound (odds ratio 2.58, 95% confidence interval 1.75 to 3.80) and Cavalier King Charles Spaniel (odds ratio 2.39, 95% confidence interval 1.85 to 3.09). Four breeds showed reduced odds compared with crossbreds. Brachycephalic breeds had 1.25 times the odds (95% confidence interval 1.11 to 1.42) of periodontal disease compared with mesocephalic breeds. Spaniel types had 1.63 times the odds (95% confidence interval 1.42 to 1.87) compared with non‐spaniel types. Increasing adult bodyweight was associated with progressively decreasing odds of periodontal disease. Clinical Significance The high prevalence identified in this study highlights periodontal disease as a priority welfare concern for predisposed breeds. Veterinarians can use this information to promote improved dental care in predisposed dogs, especially as these dogs age.
Collapse
|
27
|
Birsa N, Ule AM, Garone MG, Tsang B, Mattedi F, Chong PA, Humphrey J, Jarvis S, Pisiren M, Wilkins OG, Nosella ML, Devoy A, Bodo C, de la Fuente RF, Fisher EMC, Rosa A, Viero G, Forman-Kay JD, Schiavo G, Fratta P. FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation. SCIENCE ADVANCES 2021; 7:7/30/eabf8660. [PMID: 34290090 PMCID: PMC8294762 DOI: 10.1126/sciadv.abf8660] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/03/2021] [Indexed: 05/16/2023]
Abstract
FUsed in Sarcoma (FUS) is a multifunctional RNA binding protein (RBP). FUS mutations lead to its cytoplasmic mislocalization and cause the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Here, we use mouse and human models with endogenous ALS-associated mutations to study the early consequences of increased cytoplasmic FUS. We show that in axons, mutant FUS condensates sequester and promote the phase separation of fragile X mental retardation protein (FMRP), another RBP associated with neurodegeneration. This leads to repression of translation in mouse and human FUS-ALS motor neurons and is corroborated in vitro, where FUS and FMRP copartition and repress translation. Last, we show that translation of FMRP-bound RNAs is reduced in vivo in FUS-ALS motor neurons. Our results unravel new pathomechanisms of FUS-ALS and identify a novel paradigm by which mutations in one RBP favor the formation of condensates sequestering other RBPs, affecting crucial biological functions, such as protein translation.
Collapse
|
28
|
Midgett D, Thorn S, Awn S, Uman S, Lysyy T, Kim J, Duncan J, Humphrey J, Papademetris X, Burdick J, Sinusas A. In-vivo Measurement Of 3d Left Ventricular Myocardial Strain Using CineCT Imaging Post Myocardial Infarction And Following Intramyocardial Delivery Of Theranostic Hydrogel. J Cardiovasc Comput Tomogr 2021. [DOI: 10.1016/j.jcct.2021.06.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
29
|
Prudencio M, Humphrey J, Pickles S, Brown AL, Hill SE, Kachergus JM, Shi J, Heckman MG, Spiegel MR, Cook C, Song Y, Yue M, Daughrity LM, Carlomagno Y, Jansen-West K, de Castro CF, DeTure M, Koga S, Wang YC, Sivakumar P, Bodo C, Candalija A, Talbot K, Selvaraj BT, Burr K, Chandran S, Newcombe J, Lashley T, Hubbard I, Catalano D, Kim D, Propp N, Fennessey S, Fagegaltier D, Phatnani H, Secrier M, Fisher EM, Oskarsson B, van Blitterswijk M, Rademakers R, Graff-Radford NR, Boeve BF, Knopman DS, Petersen RC, Josephs KA, Thompson EA, Raj T, Ward M, Dickson DW, Gendron TF, Fratta P, Petrucelli L. Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia. J Clin Invest 2020; 130:6080-6092. [PMID: 32790644 PMCID: PMC7598060 DOI: 10.1172/jci139741] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
No treatment for frontotemporal dementia (FTD), the second most common type of early-onset dementia, is available, but therapeutics are being investigated to target the 2 main proteins associated with FTD pathological subtypes: TDP-43 (FTLD-TDP) and tau (FTLD-tau). Testing potential therapies in clinical trials is hampered by our inability to distinguish between patients with FTLD-TDP and FTLD-tau. Therefore, we evaluated truncated stathmin-2 (STMN2) as a proxy of TDP-43 pathology, given the reports that TDP-43 dysfunction causes truncated STMN2 accumulation. Truncated STMN2 accumulated in human induced pluripotent stem cell-derived neurons depleted of TDP-43, but not in those with pathogenic TARDBP mutations in the absence of TDP-43 aggregation or loss of nuclear protein. In RNA-Seq analyses of human brain samples from the NYGC ALS cohort, truncated STMN2 RNA was confined to tissues and disease subtypes marked by TDP-43 inclusions. Last, we validated that truncated STMN2 RNA was elevated in the frontal cortex of a cohort of patients with FTLD-TDP but not in controls or patients with progressive supranuclear palsy, a type of FTLD-tau. Further, in patients with FTLD-TDP, we observed significant associations of truncated STMN2 RNA with phosphorylated TDP-43 levels and an earlier age of disease onset. Overall, our data uncovered truncated STMN2 as a marker for TDP-43 dysfunction in FTD.
Collapse
|
30
|
Humphrey J, Birsa N, Milioto C, McLaughlin M, Ule AM, Robaldo D, Eberle AB, Kräuchi R, Bentham M, Brown AL, Jarvis S, Bodo C, Garone M, Devoy A, Soraru G, Rosa A, Bozzoni I, Fisher EMC, Mühlemann O, Schiavo G, Ruepp MD, Isaacs AM, Plagnol V, Fratta P. FUS ALS-causative mutations impair FUS autoregulation and splicing factor networks through intron retention. Nucleic Acids Res 2020; 48:6889-6905. [PMID: 32479602 PMCID: PMC7337901 DOI: 10.1093/nar/gkaa410] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/21/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in the RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease. FUS plays a role in numerous aspects of RNA metabolism, including mRNA splicing. However, the impact of ALS-causative mutations on splicing has not been fully characterized, as most disease models have been based on overexpressing mutant FUS, which will alter RNA processing due to FUS autoregulation. We and others have recently created knockin models that overcome the overexpression problem, and have generated high depth RNA-sequencing on FUS mutants in parallel to FUS knockout, allowing us to compare mutation-induced changes to genuine loss of function. We find that FUS-ALS mutations induce a widespread loss of function on expression and splicing. Specifically, we find that mutant FUS directly alters intron retention levels in RNA-binding proteins. Moreover, we identify an intron retention event in FUS itself that is associated with its autoregulation. Altered FUS levels have been linked to disease, and we show here that this novel autoregulation mechanism is altered by FUS mutations. Crucially, we also observe this phenomenon in other genetic forms of ALS, including those caused by TDP-43, VCP and SOD1 mutations, supporting the concept that multiple ALS genes interact in a regulatory network.
Collapse
|
31
|
Melvinsdottir I, Lee S, Avendano R, Midgett D, Thorn S, Liu Y, Uman S, Humphrey J, Duncan J, Burdick J, Sinusas A. Multimodality Imaging Approach To Evaluate The Delivery And Impact Of A Novel Imageable Theranostic Hydrogel Post Myocardial Infarction In A Chronic Porcine Model. J Cardiovasc Comput Tomogr 2020. [DOI: 10.1016/j.jcct.2020.06.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
32
|
Avendaño R, Midgett D, Melvinsdottir I, Lee S, Hawley C, Mamarian M, Uman S, Thorn S, Humphrey J, Duncan J, Burdick J, Sinusas A. Cardiac CT Approach To Guide Delivery And Evaluate The Impact Of A Novel Imageable Theranostic Hydrogel Post Myocardial Infarction In An Acute Porcine Model. J Cardiovasc Comput Tomogr 2020. [DOI: 10.1016/j.jcct.2020.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Bochukova EG, Lawler K, Croizier S, Keogh JM, Patel N, Strohbehn G, Lo KK, Humphrey J, Hokken-Koelega A, Damen L, Donze S, Bouret SG, Plagnol V, Farooqi IS. A Transcriptomic Signature of the Hypothalamic Response to Fasting and BDNF Deficiency in Prader-Willi Syndrome. Cell Rep 2019; 22:3401-3408. [PMID: 29590610 PMCID: PMC5896230 DOI: 10.1016/j.celrep.2018.03.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/07/2018] [Accepted: 03/05/2018] [Indexed: 01/07/2023] Open
Abstract
Transcriptional analysis of brain tissue from people with molecularly defined causes of obesity may highlight disease mechanisms and therapeutic targets. We performed RNA sequencing of hypothalamus from individuals with Prader-Willi syndrome (PWS), a genetic obesity syndrome characterized by severe hyperphagia. We found that upregulated genes overlap with the transcriptome of mouse Agrp neurons that signal hunger, while downregulated genes overlap with the expression profile of Pomc neurons activated by feeding. Downregulated genes are expressed mainly in neuronal cells and contribute to neurogenesis, neurotransmitter release, and synaptic plasticity, while upregulated, predominantly microglial genes are involved in inflammatory responses. This transcriptional signature may be mediated by reduced brain-derived neurotrophic factor expression. Additionally, we implicate disruption of alternative splicing as a potential molecular mechanism underlying neuronal dysfunction in PWS. Transcriptomic analysis of the human hypothalamus may identify neural mechanisms involved in energy homeostasis and potential therapeutic targets for weight loss. Overlap between genes expressed in human PWS hypothalamus and mouse Agrp neurons Downregulated genes are involved in neuronal development SNORD116 deletion reduces neural development and survival in cells Alternative splicing is disturbed in PWS
Collapse
|
34
|
Sivakumar P, De Giorgio F, Ule AM, Neeves J, Nair RR, Bentham M, Birsa N, Humphrey J, Plagnol V, Acevedo-Arozena A, Cunningham TJ, Fisher EMC, Fratta P. TDP-43 mutations increase HNRNP A1-7B through gain of splicing function. Brain 2019; 141:e83. [PMID: 30364928 DOI: 10.1093/brain/awy260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
35
|
Habib AM, Matsuyama A, Okorokov AL, Santana-Varela S, Bras JT, Aloisi AM, Emery EC, Bogdanov YD, Follenfant M, Gossage SJ, Gras M, Humphrey J, Kolesnikov A, Le Cann K, Li S, Minett MS, Pereira V, Ponsolles C, Sikandar S, Torres JM, Yamaoka K, Zhao J, Komine Y, Yamamori T, Maniatis N, Panov KI, Houlden H, Ramirez JD, Bennett DLH, Marsili L, Bachiocco V, Wood JN, Cox JJ. A novel human pain insensitivity disorder caused by a point mutation in ZFHX2. Brain 2019; 141:365-376. [PMID: 29253101 PMCID: PMC5837393 DOI: 10.1093/brain/awx326] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/18/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic pain is a major global public health issue causing a severe impact on both the quality of life for sufferers and the wider economy. Despite the significant clinical burden, little progress has been made in terms of therapeutic development. A unique approach to identifying new human-validated analgesic drug targets is to study rare families with inherited pain insensitivity. Here we have analysed an otherwise normal family where six affected individuals display a pain insensitive phenotype that is characterized by hyposensitivity to noxious heat and painless bone fractures. This autosomal dominant disorder is found in three generations and is not associated with a peripheral neuropathy. A novel point mutation in ZFHX2, encoding a putative transcription factor expressed in small diameter sensory neurons, was identified by whole exome sequencing that segregates with the pain insensitivity. The mutation is predicted to change an evolutionarily highly conserved arginine residue 1913 to a lysine within a homeodomain. Bacterial artificial chromosome (BAC) transgenic mice bearing the orthologous murine p.R1907K mutation, as well as Zfhx2 null mutant mice, have significant deficits in pain sensitivity. Gene expression analyses in dorsal root ganglia from mutant and wild-type mice show altered expression of genes implicated in peripheral pain mechanisms. The ZFHX2 variant and downstream regulated genes associated with a human pain-insensitive phenotype are therefore potential novel targets for the development of new analgesic drugs.awx326media15680039660001.
Collapse
|
36
|
Li YI, Wong G, Humphrey J, Raj T. Prioritizing Parkinson's disease genes using population-scale transcriptomic data. Nat Commun 2019; 10:994. [PMID: 30824768 PMCID: PMC6397174 DOI: 10.1038/s41467-019-08912-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 02/05/2019] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified over 41 susceptibility loci associated with Parkinson's Disease (PD) but identifying putative causal genes and the underlying mechanisms remains challenging. Here, we leverage large-scale transcriptomic datasets to prioritize genes that are likely to affect PD by using a transcriptome-wide association study (TWAS) approach. Using this approach, we identify 66 gene associations whose predicted expression or splicing levels in dorsolateral prefrontal cortex (DLFPC) and peripheral monocytes are significantly associated with PD risk. We uncover many novel genes associated with PD but also novel mechanisms for known associations such as MAPT, for which we find that variation in exon 3 splicing explains the common genetic association. Genes identified in our analyses belong to the same or related pathways including lysosomal and innate immune function. Overall, our study provides a strong foundation for further mechanistic studies that will elucidate the molecular drivers of PD.
Collapse
|
37
|
Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, Wang YC, Ng B, Gupta I, Haroutunian V, Schadt EE, Young-Pearse T, Mostafavi S, Zhang B, Sklar P, Bennett DA, De Jager PL. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility. Nat Genet 2018; 50:1584-1592. [PMID: 30297968 PMCID: PMC6354244 DOI: 10.1038/s41588-018-0238-1] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
Abstract
Here we use deep sequencing to identify sources of variation in mRNA splicing in the dorsolateral prefrontal cortex (DLPFC) of 450 subjects from two aging cohorts. Hundreds of aberrant pre-mRNA splicing events are reproducibly associated with Alzheimer's disease. We also generate a catalog of splicing quantitative trait loci (sQTL) effects: splicing of 3,006 genes is influenced by genetic variation. We report that altered splicing is the mechanism for the effects of the PICALM, CLU and PTK2B susceptibility alleles. Furthermore, we performed a transcriptome-wide association study and identified 21 genes with significant associations with Alzheimer's disease, many of which are found in known loci, whereas 8 are in novel loci. These results highlight the convergence of old and new genes associated with Alzheimer's disease in autophagy-lysosomal-related pathways. Overall, this study of the transcriptome of the aging brain provides evidence that dysregulation of mRNA splicing is a feature of Alzheimer's disease and is, in some cases, genetically driven.
Collapse
|
38
|
Fratta P, Sivakumar P, Humphrey J, Lo K, Ricketts T, Oliveira H, Brito-Armas JM, Kalmar B, Ule A, Yu Y, Birsa N, Bodo C, Collins T, Conicella AE, Mejia Maza A, Marrero-Gagliardi A, Stewart M, Mianne J, Corrochano S, Emmett W, Codner G, Groves M, Fukumura R, Gondo Y, Lythgoe M, Pauws E, Peskett E, Stanier P, Teboul L, Hallegger M, Calvo A, Chiò A, Isaacs AM, Fawzi NL, Wang E, Housman DE, Baralle F, Greensmith L, Buratti E, Plagnol V, Fisher EM, Acevedo-Arozena A. Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis. EMBO J 2018; 37:embj.201798684. [PMID: 29764981 PMCID: PMC5983119 DOI: 10.15252/embj.201798684] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/15/2018] [Accepted: 03/22/2018] [Indexed: 12/11/2022] Open
Abstract
TDP‐43 (encoded by the gene TARDBP) is an RNA binding protein central to the pathogenesis of amyotrophic lateral sclerosis (ALS). However, how TARDBP mutations trigger pathogenesis remains unknown. Here, we use novel mouse mutants carrying point mutations in endogenous Tardbp to dissect TDP‐43 function at physiological levels both in vitro and in vivo. Interestingly, we find that mutations within the C‐terminal domain of TDP‐43 lead to a gain of splicing function. Using two different strains, we are able to separate TDP‐43 loss‐ and gain‐of‐function effects. TDP‐43 gain‐of‐function effects in these mice reveal a novel category of splicing events controlled by TDP‐43, referred to as “skiptic” exons, in which skipping of constitutive exons causes changes in gene expression. In vivo, this gain‐of‐function mutation in endogenous Tardbp causes an adult‐onset neuromuscular phenotype accompanied by motor neuron loss and neurodegenerative changes. Furthermore, we have validated the splicing gain‐of‐function and skiptic exons in ALS patient‐derived cells. Our findings provide a novel pathogenic mechanism and highlight how TDP‐43 gain of function and loss of function affect RNA processing differently, suggesting they may act at different disease stages.
Collapse
|
39
|
Sivakumar P, Humphrey J, Lo K, Ricketts T, Oliveira H, Kalmar B, Wang E, Housman D, Baralle F, Greensmith L, Buratti E, Plagnol V, Fisher E, Arozena A, Fratta P. Dissecting TDP-43 gain- and loss-of-function in neurodegeneration. Neuromuscul Disord 2018. [DOI: 10.1016/s0960-8966(18)30366-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
40
|
Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK. Annotation-free quantification of RNA splicing using LeafCutter. Nat Genet 2018; 50:151-158. [PMID: 29229983 PMCID: PMC5742080 DOI: 10.1038/s41588-017-0004-9] [Citation(s) in RCA: 347] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/08/2017] [Indexed: 01/15/2023]
Abstract
The excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable splicing events from short-read RNA-seq data and finds events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both to detect differential splicing between sample groups and to map splicing quantitative trait loci (sQTLs). Compared with contemporary methods, our approach identified 1.4-2.1 times more sQTLs, many of which helped us ascribe molecular effects to disease-associated variants. Transcriptome-wide associations between LeafCutter intron quantifications and 40 complex traits increased the number of associated disease genes at a 5% false discovery rate by an average of 2.1-fold compared with that detected through the use of gene expression levels alone. LeafCutter is fast, scalable, easy to use, and available online.
Collapse
|
41
|
Lapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugedara G, Humphrey J, DeBARRY JD, Le Roch KG, Galinski MR, Kissinger JC. PacBio assembly of a Plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family. Parasitology 2018; 145:71-84. [PMID: 28720171 PMCID: PMC5798397 DOI: 10.1017/s0031182017001329] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 12/20/2022]
Abstract
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features. Today, long-read PacBio and chromatin conformation technologies are overcoming such obstacles. Here, based on the use of these technologies, we present a highly refined de novo P. knowlesi genome sequence of the Pk1(A+) clone. This sequence and annotation, referred to as the 'MaHPIC Pk genome sequence', includes manual annotation of the SICAvar gene family with 136 full-length members categorized as type I or II. This sequence provides a framework that will permit a better understanding of the SICAvar repertoire, selective pressures acting on this gene family and mechanisms of antigenic variation in this species and other pathogens.
Collapse
|
42
|
Devoy A, Kalmar B, Stewart M, Park H, Burke B, Noy SJ, Redhead Y, Humphrey J, Lo K, Jaeger J, Mejia Maza A, Sivakumar P, Bertolin C, Soraru G, Plagnol V, Greensmith L, Acevedo Arozena A, Isaacs AM, Davies B, Fratta P, Fisher EMC. Humanized mutant FUS drives progressive motor neuron degeneration without aggregation in 'FUSDelta14' knockin mice. Brain 2017; 140:2797-2805. [PMID: 29053787 PMCID: PMC5841203 DOI: 10.1093/brain/awx248] [Citation(s) in RCA: 73] [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: 04/06/2017] [Revised: 07/16/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022] Open
Abstract
Mutations in FUS are causative for amyotrophic lateral sclerosis with a dominant mode of inheritance. In trying to model FUS-amyotrophic lateral sclerosis (ALS) in mouse it is clear that FUS is dosage-sensitive and effects arise from overexpression per se in transgenic strains. Novel models are required that maintain physiological levels of FUS expression and that recapitulate the human disease-with progressive loss of motor neurons in heterozygous animals. Here, we describe a new humanized FUS-ALS mouse with a frameshift mutation, which fulfils both criteria: the FUS Delta14 mouse. Heterozygous animals express mutant humanized FUS protein at physiological levels and have adult onset progressive motor neuron loss and denervation of neuromuscular junctions. Additionally, we generated a novel antibody to the unique human frameshift peptide epitope, allowing specific identification of mutant FUS only. Using our new FUSDelta14 ALS mouse-antibody system we show that neurodegeneration occurs in the absence of FUS protein aggregation. FUS mislocalization increases as disease progresses, and mutant FUS accumulates at the rough endoplasmic reticulum. Further, transcriptomic analyses show progressive changes in ribosomal protein levels and mitochondrial function as early disease stages are initiated. Thus, our new physiological mouse model has provided novel insight into the early pathogenesis of FUS-ALS.
Collapse
|
43
|
Humphrey J, Emmett W, Fratta P, Isaacs AM, Plagnol V. Quantitative analysis of cryptic splicing associated with TDP-43 depletion. BMC Med Genomics 2017; 10:38. [PMID: 28549443 PMCID: PMC5446763 DOI: 10.1186/s12920-017-0274-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/17/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. METHODS We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. RESULTS We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. CONCLUSIONS Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.
Collapse
|
44
|
Sivakumar P, Humphrey J, Ule A, Bodo C, Emmett W, Ricketts T, Oliveira H, Wang E, Housman D, Greensmith L, Buratti E, Baralle F, Plagnol V, Acevedo-Arozena A, Fisher E, Fratta P. Investigating dysfunctional RNA processing in TDP-43 mouse mutants. Neuromuscul Disord 2017. [DOI: 10.1016/s0960-8966(17)30314-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
45
|
Olby NJ, Muguet-Chanoit AC, Lim JH, Davidian M, Mariani CL, Freeman AC, Platt SR, Humphrey J, Kent M, Giovanella C, Longshore R, Early PJ, Muñana KR. A Placebo-Controlled, Prospective, Randomized Clinical Trial of Polyethylene Glycol and Methylprednisolone Sodium Succinate in Dogs with Intervertebral Disk Herniation. J Vet Intern Med 2016; 30:206-14. [PMID: 26520829 PMCID: PMC4913663 DOI: 10.1111/jvim.13657] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Acute intervertebral disk herniation (IVDH) is a common cause of spinal cord injury in dogs and currently there is no proven medical treatment to counter secondary injury effects. Use of methylprednisolone sodium succinate (MPSS) or polyethylene glycol (PEG) as neuroprotectants is advocated but controversial because neither treatment has been tested in placebo-controlled, randomized, blinded trials in dogs. HYPOTHESIS Polyethylene glycol will improve the outcome of severe spinal cord injury caused by IVDH compared to MPSS or placebo. ANIMALS Client-owned dogs with acute onset of thoracolumbar IVDH causing paralysis and loss of nociception for <24 hours. METHODS Dogs were randomized to receive MPSS, PEG, or placebo; drugs appeared identical and group allocation was masked. Drug administration was initiated once the diagnosis of IVDH was confirmed and all dogs underwent hemilaminectomy. Neurologic function was assessed 2, 4, 8, and 12 weeks postoperatively using an open field gait score (OFS) as the primary outcome measure. Outcomes were compared by the Wilcoxon rank sum test. RESULTS Sixty-three dogs were recruited and 47.6% recovered ambulation. 17.5% developed progressive myelomalacia but there was no association with group. There was no difference in OFS among groups. Although full study power was not reached, conditional power analyses indicated the futility of continued case recruitment. CONCLUSIONS This clinical trial did not show a benefit of either MPSS or PEG in the treatment of acute, severe thoracolumbar IVDH when used as adjunctive medical treatment administered to dogs presenting within 24 hours of onset of paralysis.
Collapse
|
46
|
Matare C, Mbuya M, Dickin K, Humphrey J, Stoltzfus R. Social Support and Depressive Symptoms Predict Adherence To Iron And Folic Acid Supplements Among Pregnant Women In Rural Zimbabwe. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.729.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
47
|
Kambarami R, Mbuya M, Humphrey J, Stoltzfus R. Determinants of Community Health Worker Performance in Nutrition Education in a Multi‐tasked Setting in Rural Zimbabwe. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.898.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
48
|
Sawyer MM, Myers G, Humphrey J, Chandler M. Trauma and Thrombelastography. Semin Cardiothorac Vasc Anesth 2012; 16:142-52. [DOI: 10.1177/1089253212446994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Bleeding disorders associated with trauma are of paramount importance when dealing with the acutely injured individual. Statistically, up to 40% of trauma related deaths are assumed to be related to hemorrhage.1,2 Historically, there have been many varying positions on the way to handle this entity.3–5 Ironically, it is not always the injury but the physiologic sequelae of that injury that lead to trauma associated deaths.6,7 Over time, newer theories have been developed to help the clinician begin to understand the etiology and treatment of this process.6,8,9 The purpose of this paper is to review current literature and explain how these new concepts helped change practice in an urban, academic, Level One Trauma Center.
Collapse
|
49
|
Marchese M, Sinisi M, Anand P, Di Mascio L, Humphrey J. Neuropathic pain following hip resurfacing due to a transneural suture. THE JOURNAL OF BONE AND JOINT SURGERY. BRITISH VOLUME 2011; 93:555-7. [PMID: 21464500 DOI: 10.1302/0301-620x.93b4.26052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A 60-year-old man developed severe neuropathic pain and foot-drop in his left leg following resurfacing arthroplasty of the left hip. The pain was refractory to all analgesics for 16 months. At exploration, a PDS suture was found passing through the sciatic nerve at several points over 6 cm and terminating in a large knot. After release of the suture and neurolysis there was dramatic and rapid improvement of the neuropathic pain and of motor function. This case represents the human equivalent of previously described nerve ligation in an animal model of neuropathic pain. It emphasises that when neuropathic pain is present after an operation, the nerve related to the symptoms must be inspected, and that removal of a suture or irritant may lead to relief of pain, even after many months.
Collapse
|
50
|
Crawford F, Wood M, Ferguson S, Mathura V, Gupta P, Humphrey J, Mouzon B, Laporte V, Margenthaler E, O'Steen B, Hayes R, Roses A, Mullan M. Apolipoprotein E-genotype dependent hippocampal and cortical responses to traumatic brain injury. Neuroscience 2009; 159:1349-62. [DOI: 10.1016/j.neuroscience.2009.01.033] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/14/2009] [Accepted: 01/19/2009] [Indexed: 11/24/2022]
|