New approaches towards understanding trypanosome mitosis

The protozoan parasite, Trypanosoma brucei has an unusual genome, consisting of an unusually large number of chromosomes. It is composed of 11 large diploid chromosomes and over 100 small linear chromosomes, known as intermediate chromosomes and minichromosomes. These smaller chromosomes contain a portion of a library of genes required for antigenic variation and, therefore, evasion of the host’s immune response. Despite their number, all chromosomes are separated with fidelity during mitosis, through interaction with the mitotic spindle. Animal and fungal model organisms have been widely used to study mitosis and the proteins involved. T. brucei, however, belongs to a group of organisms that diverged from the animal-fungus lineage at or close to the eukaryotic root. Mitosis in trypanosomes differs from that observed in model organisms, including an apparent lack of conserved microtubule motor proteins that drive spindle function and a reduced number of kinetochores. It is, therefore, not well understood how trypanosomes segregate their genomes. In this thesis, I will present the development of an RNA interference based library methodology for the investigation of microtubule motor function. This system uses a combinatorial library that accounts for interactions, such as redundancy, which can occur between motors. I demonstrate that motor redundancy can occur in trypanosomes, by knocking down flagellar kinesin-2 motors. The library approach allows for exploration of an individual motor’s contribution to fitness and, by combining the library with a negative selection marker tag of individual chromosomes, the motor’s role in chromosome segregation. The use of a negative selection marker also allows for quantification of chromosome loss, as I demonstrate by quantifying the losses caused by depletion of the mitotic motor KIN13-1 and the kinetochore protein KKIP1. I also present the development of a cell line to be used in validating the results of the library experiments. The production of a tag that uses KIN13-1 to label the mitotic spindle, for later observations of spindle defects, is presented. Finally, I present the development of a chromosome label that uses arrays of Lac operator repeats and fluorescently labelled Lac repressor protein to tag DNA elements, to follow chromosomes through the cell cycle. I demonstrate this label’s use in detecting chromosome loss and non-disjunction events after knockdown of KIN13-1 and KKIP1. I then use it to demonstrate interactions between chromosomes and kinetochores during mitosis. These data provide evidence that refutes a “lateral stacking” model for chromosome segregation

Effects of carbamazepine and lamotrigine on functional magnetic resonance imaging cognitive networks.

OBJECTIVE: To investigate the effects of sodium channel-blocking antiepileptic drugs (AEDs) on functional magnetic resonance imaging (fMRI) language network activations in patients with focal epilepsy. METHODS: In a retrospective study, we identified patients who were treated at the time of language fMRI scanning with either carbamazepine (CBZ; n = 42) or lamotrigine (LTG; n = 42), but not another sodium channel-blocking AED. We propensity-matched 42 patients taking levetiracetam (LEV) as "patient-controls" and included further 42 age- and gender-matched healthy controls. After controlling for age, age at onset of epilepsy, gender, and antiepileptic comedications, we compared verbal fluency fMRI activations between groups and out-of-scanner psychometric measures of verbal fluency. RESULTS: Patients on CBZ performed less well on a verbal fluency tests than those taking LTG or LEV. Compared to either LEV-treated patients or controls, patients taking CBZ showed decreased activations in left inferior frontal gyrus and patients on LTG showed abnormal deactivations in frontal and parietal default mode areas. All patient groups showed fewer activations in the putamen bilaterally compared to controls. In a post hoc analysis, out-of-scanner fluency scores correlated positively with left putamen activation. SIGNIFICANCE: Our study provides evidence of AED effects on the functional neuroanatomy of language, which might explain subtle language deficits in patients taking otherwise well-tolerated sodium channel-blocking agents. Patients on CBZ showed dysfunctional frontal activation and more pronounced impairment of performance than patients taking LTG, which was associated only with failure to deactivate task-negative networks. As previously shown for working memory, LEV treatment did not affect functional language networks

Use of humanised rat basophilic leukaemia cell line RS-ATL8 for the assessment of allergenicity of Schistosoma mansoni proteins.

BACKGROUND Parasite-specific IgE is thought to correlate with protection against Schistosoma mansoni infection or re-infection. Only a few molecular targets of the IgE response in S. mansoni infection have been characterised. A better insight into the basic mechanisms of anti-parasite immunity could be gained from a genome-wide characterisation of such S. mansoni allergens. This would have repercussions on our understanding of allergy and the development of safe and efficacious vaccinations against helminthic parasites. METHODOLOGY/PRINCIPAL FINDINGS A complete medium- to high-throughput amenable workflow, including important quality controls, is described, which enables the rapid translation of S. mansoni proteins using wheat germ lysate and subsequent assessment of potential allergenicity with a humanised Rat Basophilic Leukemia (RBL) reporter cell line. Cell-free translation is completed within 90 minutes, generating sufficient amounts of parasitic protein for rapid screening of allergenicity without any need for purification. Antigenic integrity is demonstrated using Western Blotting. After overnight incubation with infected individuals' serum, the RS-ATL8 reporter cell line is challenged with the complete wheat germ translation mixture and Luciferase activity measured, reporting cellular activation by the suspected allergen. The suitability of this system for characterization of novel S. mansoni allergens is demonstrated using well characterised plant and parasitic allergens such as Par j 2, SmTAL-1 and the IgE binding factor IPSE/alpha-1, expressed in wheat germ lysates and/or E. coli. SmTAL-1, but not SmTAL2 (used as a negative control), was able to activate the basophil reporter cell line. CONCLUSION/SIGNIFICANCE This method offers an accessible way for assessment of potential allergenicity of anti-helminthic vaccine candidates and is suitable for medium- to high-throughput studies using infected individual sera. It is also suitable for the study of the basis of allergenicity of helminthic proteins

Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer's Disease

Background 1Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P ≤ 1 × 10−5. We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 × 10−17; including ADGC data, meta P = 5.0 × 10−21) and the MS4A gene cluster (rs610932, meta P = 1.8 × 10−14; including ADGC data, meta P = 1.2 × 10−16) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 × 10−4; including ADGC data, meta P = 8.6 × 10−9), CD33 (GERAD+, P = 2.2 × 10−4; including ADGC data, meta P = 1.6 × 10−9) and EPHA1 (GERAD+, P = 3.4 × 10−4; including ADGC data, meta P = 6.0 × 10−10)

Correction: genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer's disease.

[This corrects the article on p. e13950 in vol. 5.]. Background: Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology: We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset. Principal Findings: We found a significant overrepresentation of association signals in pathways related to cholesterol metabolism and the immune response in both of the two largest genome-wide association studies for LOAD. Significance: Processes related to cholesterol metabolism and the innate immune response have previously been implicated by pathological and epidemiological studies of Alzheimer's disease, but it has been unclear whether those findings reflected primary aetiological events or consequences of the disease process. Our independent evidence from two large studies now demonstrates that these processes are aetiologically relevant, and suggests that they may be suitable targets for novel and existing therapeutic approaches

A novel Alzheimer disease locus located near the gene encoding tau protein

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordAPOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ε4+ (10 352 cases and 9207 controls) and APOE ε4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ε4 status. Suggestive associations (P<1 × 10-4) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ε4+: 1250 cases and 536 controls; APOE ε4-: 718 cases and 1699 controls). Among APOE ε4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10-9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10-7) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P≤1.3 × 10-8), frontal cortex (P≤1.3 × 10-9) and temporal cortex (P≤1.2 × 10-11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10-6) and temporal cortex (P=2.6 × 10-6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted

New approaches towards understanding trypanosome mitosis

The protozoan parasite, Trypanosoma brucei has an unusual genome, consisting of an unusually large number of chromosomes. It is composed of 11 large diploid chromosomes and over 100 small linear chromosomes, known as intermediate chromosomes and minichromosomes. These smaller chromosomes contain a portion of a library of genes required for antigenic variation and, therefore, evasion of the host’s immune response. Despite their number, all chromosomes are separated with fidelity during mitosis, through interaction with the mitotic spindle. Animal and fungal model organisms have been widely used to study mitosis and the proteins involved. T. brucei, however, belongs to a group of organisms that diverged from the animal-fungus lineage at or close to the eukaryotic root. Mitosis in trypanosomes differs from that observed in model organisms, including an apparent lack of conserved microtubule motor proteins that drive spindle function and a reduced number of kinetochores. It is, therefore, not well understood how trypanosomes segregate their genomes. In this thesis, I will present the development of an RNA interference based library methodology for the investigation of microtubule motor function. This system uses a combinatorial library that accounts for interactions, such as redundancy, which can occur between motors. I demonstrate that motor redundancy can occur in trypanosomes, by knocking down flagellar kinesin-2 motors. The library approach allows for exploration of an individual motor’s contribution to fitness and, by combining the library with a negative selection marker tag of individual chromosomes, the motor’s role in chromosome segregation. The use of a negative selection marker also allows for quantification of chromosome loss, as I demonstrate by quantifying the losses caused by depletion of the mitotic motor KIN13-1 and the kinetochore protein KKIP1. I also present the development of a cell line to be used in validating the results of the library experiments. The production of a tag that uses KIN13-1 to label the mitotic spindle, for later observations of spindle defects, is presented. Finally, I present the development of a chromosome label that uses arrays of Lac operator repeats and fluorescently labelled Lac repressor protein to tag DNA elements, to follow chromosomes through the cell cycle. I demonstrate this label’s use in detecting chromosome loss and non-disjunction events after knockdown of KIN13-1 and KKIP1. I then use it to demonstrate interactions between chromosomes and kinetochores during mitosis. These data provide evidence that refutes a “lateral stacking” model for chromosome segregation