Choline Nutriture in Phenylketonuria: Metabolomic Patterns, Dietary Determinants, and Implications for Cognitive Performance Restricted; Files Only

Schoen, Meriah (Fall 2022)

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While the severe neurocognitive consequences of Phenylketonuria (PKU) can now be prevented, cognitive deficits are still common in early-treated individuals and cannot be solely attributed to elevated phenylalanine (Phe) concentrations. The purpose of this dissertation was to identify and evaluate an alternate source of cognitive variability in PKU.

First, we performed untargeted metabolomics in females with PKU to examine metabolic perturbations, beyond Phe, that could be contributing to phenotypic variability. PKU plasma metabolite profiles were examined relative to matched controls, and after a 5-day camp intervention. This analysis identified perturbations in choline-containing compounds, which have not been observed before, in addition to notable alterations in fatty acid and amino acid metabolites. These pathways, which could reflect bioenergetic impairment and oxidative stress, improved or fully normalized with positive changes in dietary adherence following a camp intervention. 

Based on these metabolomics results, and prior evidence for a positive relationship between choline and cognition, we then characterized usual choline intake distributions in adults and children with PKU. This analysis found that choline adequacy was suboptimal among individuals with PKU [only 10.8% achieved the adequate intake (AI)], but improved with the use of pharmacotherapies that allow for partially-restricted or fully-unrestricted protein intake. Choline fortified medical foods were required to achieve the AI among individuals maintaining a Phe-restricted diet.

To determine the functional effects of suboptimal choline intake, we evaluated the relationship between total choline intake and working memory performance in early-treated adults with PKU and demographically matched controls. Across the full sample, working memory performance did not differ based on choline intake, and this pattern was not modified by diagnosis. Nevertheless, working memory performance was positively associated with concurrent total choline intake in a subsample of PKU participants with optimal metabolic control in middle childhood and adulthood.

Overall, this dissertation substantiates choline as a nutrient of concern in PKU and suggests that suboptimal choline nutriture may be contributing to the cognitive variability in early-treated individuals with PKU. To confirm and build upon these findings, larger observational studies and controlled trials are needed, in addition to more frequent clinical monitoring of choline intake.

Table of Contents


1.1 References. 4


2.1 Epidemiology and Diagnosis of PKU. 6

2.2 Pathophysiology of PKU. 7

2.3 Neurocognitive Profile of Early-Treated PKU. 9

2.4 Variability in the Cognitive Profiles of Early-Treated Individuals with PKU. 10

2.5 Metabolomics Approaches to Investigate Phenotypic Variability in PKU. 11

2.6 Suboptimal Nutriture as a Source of Phenotypic Variability in PKU. 12

2.7 Functions and Metabolism of Choline. 14

2.8 Maintenance of Choline Nutriture. 14

2.9 Choline Needs May Be Higher in PKU. 15

2.10 Choline Nutriture May Contribute to the Pathophysiology of PKU. 17

2.11 Choline Nutriture May Affect Cognitive Performance PKU. 17

2.12 Summary and Overall Significance. 19

2.11 References. 20


3.1 Overview of Study Cohorts. 34

3.1.1 PKU Cohorts. 34

3.1.2 Control Cohorts. 38

3.2 Dietary Assessment Methods. 39

3.2.1 Collection of Dietary Intake Data. 39

3.2.2 Nutrient Analysis. 40

3.2.3 Estimating Mean Nutrient Intake. 41

3.2.4 Estimating the Distribution of Usual Intake. 41

3.3 Cognitive Assessment Methods. 42

3.3.1 Assessment of Overall Intellectual Functioning. 43

3.3.2 Assessment of Visuospatial and Verbal Working Memory. 43

3.3.3 Assessment of Verbal Working Memory. 44

3.4 Collection of Historical Phenylalanine Records. 45

3.5 References. 47

CHAPTER 4: Plasma Metabolomic Profile Changes in Females with Phenylketonuria (PKU) Following a Camp Intervention. 51

4.1 Abstract. 51

4.2 Introduction. 54

4.3 Methods. 55

4.3.1 Sample and Study Design. 55

4.3.2 Data Collection. 56

4.3.3 Metabolomics Analysis. 57

4.3.4 Data Processing and Statistical Analysis. 58

4.3.5 Data Visualization and Differential Abundance Analysis. 58

4.3.6 Pathway Analysis and Feature Selection. 59

4.3.7 Diet and Metabolite Correlations. 60

4.4 Results. 60

4.4.1 Baseline Plasma Metabolome based on Disease State, Treatment Status, and Age Group. 61

4.4.2 Changes in Biochemical Control and Dietary Composition Associated with  Metabolic Camp Intervention. 62

4.4.3 Changes in the PKU Plasma Metabolome Associated with Metabolic Camp Intervention. 63

4.4.4 Correlations between Nutrient Intake and Metabolite Changes. 64

4.5 Discussion. 64

4.6 References. 70

4.7 Tables and Figures. 76

4.8 Supplementary Tables and Figures. 84

CHAPTER 5: Characterization of Choline Nutriture Among Adults and Children with Phenylketonuria. 88

5.1 Abstract. 89

5.2 Introduction. 90

5.3 Materials and Methods. 92

5.3.1 Study Participants. 92

5.3.2 Quantification of Nutrient Intake from Food and Supplemental Sources. 93

5.3.3 Estimation of Usual Intake. 94

5.3.4 Estimation of Nutrient Probability of Adequacy. 95

5.3.5 Statistical Analysis. 95

5.4 Results. 96

5.4.1 Estimated Usual Choline Intake. 97

5.4.2 Mean Probability of Adequacy (MPA) for Nutrients that Affect Choline Metabolism. 98

5.5 Discussion. 99

5.6 Conclusions. 102

5.5 References. 104

5.6 Tables and Figures. 112

5.7 Supplementary Tables and Figures. 118

CHAPTER 6: Total Choline Intake and Working Memory Performance in Adults with Phenylketonuria. 119

6.1 Abstract. 120

6.2 Introduction. 122

6.3 Materials and Methods. 124

6.3.1 Participants. 124

6.3.2 Design and Procedure. 125

6.3.3 Generation of a Working Memory Composite. 126

6.3.4 Assessment of Total Choline Intakes. 126

6.3.5 Metabolic Control Measures. 127

6.3.6 Statistical Analysis. 127

6.4 Results. 129

6.4.1 Comparison of Working Memory Performance Between Participants with PKU and Controls. 130

6.4.2 Relationship between Working Memory Performance and Metabolic Control. 130

6.4.3 Relationship between Total Choline Intake, Diagnosis, and Working Memory Performance. 131

6.4.4 Relationship between Total Choline Intake, Metabolic Control, and Working Memory Performance. 131

6.5 Discussion. 133

6.6 Conclusions. 137

6.7 References. 138

6.8 Tables and Figures. 145


7.1 Key Findings. 154

7.2 Strengths and Limitations. 155

7.3 Clinical and Public Health Implications. 158

7.4 Future Directions for Research. 159

7.5 References. 162

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