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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2021)

The widespread adoption of genome-wide association studies (GWAS) has revolutionized the detection of genetic loci associated with complex traits. However, the majority of common susceptibility loci reside in poorly annotated noncoding genomic regions and are composed of many correlated polymorphisms due to linkage disequilibrium, obscuring identification of the causal variants and mechanisms underlying trait association. Thus, the functional annotation of noncoding variation is a major impediment to interpretation of genetic risk. Massively Parallel Reporter Assays (MPRA) are a novel experimental approach for the high-throughput functional characterization of noncoding genetic variation, yet remain to be systematically applied to any neurologic disorder. In this dissertation, I utilize MPRA to characterize variation associated with two neurodegenerative disorders that share tau-protein neuropathology, Alzheimer’s disease and Progressive Supranuclear Palsy. First, I describe the design and implementation of an MPRA to screen 5,706 noncoding variants derived from three GWAS for AD and PSP, identifying 320 regulatory polymorphisms comprising 27 of 34 tested loci. These results enable subsequent identification of novel putative risk genes including PLEKHM1 and APOC1 distributed across the complex 17q21.31 and 19q13.32 regions. In Chapter 3, I show that functional predictions from four popular computational algorithms for variant prioritization are discordant both with MPRA results and each other. In Chapter 4, I find that MPRA-defined functional variants preferentially disrupt predicted transcription factor binding sites that converge on enhancers with differential cell-type specific activity in PSP and AD, implicating a neuronal SP1-driven regulatory network in PSP pathogenesis. These analyses support a novel mechanism underlying noncoding genetic risk, whereby common genetic variants drive disease risk via their aggregate activity on specific transcriptional programs. In Chapter 5, I perform genome editing to validate four causal loci, identifying C4 as a novel genetic risk factor for AD. Finally, in Chapter 6, I interrogate technical parameters relevant to assay performance, aiding future studies. Taken together, this work represents a comprehensive characterization of common genetic risk associated with AD and PSP and implicates variants, genes, and transcriptional regulatory networks that represent novel risk factors for neurodegenerative tauopathies.

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Cover page: Systematic Characterization of Tauopathy-Associated Genetic Risk Loci using Multiplexed Reporter Assays
  • Article
  • Peer Reviewed
UCLA Previously Published Works (2018)

Objective

To perform a systematic review and meta-analysis of real-world evidence for the use of low-frequency repetitive transcranial magnetic stimulation (rTMS) in the treatment of drug-resistant epilepsy.

Methods

We systematically searched PubMed, Scopus, Medline, and clinicaltrials.gov for all relevant articles. Relevant patient and stimulation predictors as well as seizure outcomes were assessed. For studies with and without individual participant data (IPD), the primary outcomes were the rate of "favorable response" (reduction in seizure frequency ≥50%) and pooled event rate of mean reduction in seizure frequency, respectively. Outcomes were assessed with comparative statistics and random-effects meta-analysis models.

Results

Of 3,477 identified articles, 12 met eligibility and were included in this review. We were able to obtain IPD for 5 articles constituting 34 participants. Univariate analysis on IPD identified greater favorable response event rates between participants with temporal seizure focus versus extratemporal (50% vs. 14%, p = 0.045) and between participants who were stimulated with a figure-8 coil versus other types (47% vs. 0%, p = 0.01). We also performed study-level meta-analysis on the remaining 7 studies without IPD, which included 212 participants. The pooled mean event rate of 50% seizure reduction using low-frequency rTMS was 30% (95% confidence interval [CI] 12-57%). Sensitivity analysis revealed that studies with a mean age ≤21 years and studies using targeted stimulation had the highest seizure reduction rates compared to studies with a mean age >21 years (69% vs. 18%) and not using a targeted stimulation (47% vs. 14-20%). Moreover, we identified high interstudy heterogeneity, moderate study bias, and high publication bias.

Significance

Real-world evidence suggests that low-frequency rTMS using a figure-8 coil may be an effective therapy for the treatment of drug-resistant epilepsy in pediatric patients. This meta-analysis can inform the design and expedite recruitment of a subsequent randomized clinical trial.
    Cover page: Repetitive transcranial magnetic stimulation for the treatment of drug‐resistant epilepsy: A systematic review and individual participant data meta‐analysis of real‐world evidence
    • Article
    • Peer Reviewed
    UCLA Previously Published Works (2018)

    Objective

    Changes in progranulin (GRN) expression have been hypothesized to alter risk for Alzheimer's disease (AD). We investigated the relationship between GRN expression in peripheral blood and clinical diagnosis of AD and mild cognitive impairment (MCI).

    Methods

    Peripheral blood progranulin gene expression was measured, using microarrays from Alzheimer's (n = 186), MCI (n = 118), and control (n = 204) subjects from the University of California San Francisco Memory and Aging Center (UCSF-MAC) and two independent published series (AddNeuroMed and ADNI). GRN gene expression was correlated with clinical, demographic, and genetic data, including APOE haplotype and the GRN rs5848 single-nucleotide polymorphism. Finally, we assessed progranulin protein levels, using enzyme-linked immunosorbent assay, and methylation status using methylation microarrays.

    Results

    We observed an increase in blood progranulin gene expression and a decrease in GRN promoter methylation in males (P = 0.007). Progranulin expression was 13% higher in AD and MCI patients compared with controls in the UCSF-MAC cohort (F2,505 = 10.41, P = 3.72*10-5). This finding was replicated in the AddNeuroMed (F2,271 = 17.9, P = 4.83*10-8) but not the ADNI series. The rs5848 SNP (T-allele) predicted decreased blood progranulin gene expression (P = 0.03). The APOE4 haplotype was positively associated with progranulin expression independent of diagnosis (P = 0.04). Finally, we did not identify differences in plasma progranulin protein levels or gene methylation between diagnostic categories.

    Interpretation

    Progranulin mRNA is elevated in peripheral blood of patients with AD and MCI and its expression is associated with numerous genetic and demographic factors. These data suggest a role in the pathogenesis of neurodegenerative dementias besides frontotemporal dementia.
      Cover page: Progranulin levels in blood in Alzheimer's disease and mild cognitive impairment
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2018)
      Variants of TREM2 are associated with Alzheimer's disease (AD). To study whether increasing TREM2 gene dosage could modify the disease pathogenesis, we developed BAC transgenic mice expressing human TREM2 (BAC-TREM2) in microglia. We found that elevated TREM2 expression reduced amyloid burden in the 5xFAD mouse model. Transcriptomic profiling demonstrated that increasing TREM2 levels conferred a rescuing effect, which includes dampening the expression of multiple disease-associated microglial genes and augmenting downregulated neuronal genes. Interestingly, 5xFAD/BAC-TREM2 mice showed further upregulation of several reactive microglial genes linked to phagocytosis and negative regulation of immune cell activation. Moreover, these mice showed enhanced process ramification and phagocytic marker expression in plaque-associated microglia and reduced neuritic dystrophy. Finally, elevated TREM2 gene dosage led to improved memory performance in AD models. In summary, our study shows that a genomic transgene-driven increase in TREM2 expression reprograms microglia responsivity and ameliorates neuropathological and behavioral deficits in AD mouse models.
        Cover page: Elevated TREM2 Gene Dosage Reprograms Microglia Responsivity and Ameliorates Pathological Phenotypes in Alzheimer's Disease Models.
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2018)
        Alzheimer's disease (AD), the most common form of dementia, is characterized by the abnormal accumulation of amyloid plaques and hyperphosphorylated tau aggregates, as well as microgliosis. Hemizygous missense variants in Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) are associated with elevated risk for developing late-onset AD. These variants are hypothesized to result in loss of function, mimicking TREM2 haploinsufficiency. However, the consequences of TREM2 haploinsufficiency on tau pathology and microglial function remain unknown. We report the effects of partial and complete loss of TREM2 on microglial function and tau-associated deficits. In vivo imaging revealed that microglia from aged TREM2-haploinsufficient mice show a greater impairment in their injury response compared with microglia from aged TREM2-KO mice. In transgenic mice expressing mutant human tau, TREM2 haploinsufficiency, but not complete loss of TREM2, increased tau pathology. In addition, whereas complete TREM2 deficiency protected against tau-mediated microglial activation and atrophy, TREM2 haploinsufficiency elevated expression of proinflammatory markers and exacerbated atrophy at a late stage of disease. The differential effects of partial and complete loss of TREM2 on microglial function and tau pathology provide important insights into the critical role of TREM2 in AD pathogenesis.
          Cover page: Differential effects of partial and complete loss of TREM2 on microglial injury response and tauopathy
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