Differential regulation of Peroxisome Proliferator Activating Receptors (PPARs) via host and microbial derived processes Open Access
Druzak, Samuel (Fall 2022)
Abstract
Nuclear receptors (NRs) are a highly conserved group of ligand regulated transcription factors. In
humans there are 48 members with each member playing unique complementary roles that allow
for generation and maintenance of multicellular life. The peroxisome proliferator-activated
(PPARs) subfamily of NRs regulate metabolism, inflammation, and proliferation, making them
attractive targets to modulate metabolic syndrome, inflammatory disease, and cancer. Many drugs
have been successfully developed to target these receptors specifically to treat metabolic disease
(i.e. fibrates and glitazones). While much of the therapeutic potential of PPARs has been realized,
undesired tissue specific effects as well as an inability to treat the underlying cause of metabolic
disease limit the utility of these treatments and have stifled development of new PPAR modulators.
To address these problems, this present work seeks to elucidate novel mechanisms by which host
proteins and microbes regulate PPARs. We began our characterization by investigating the
mechanism by which PPARs acquire ligand. Previously, our lab has demonstrated that FABP5
enhances PPARδ transactivation in a polyunsaturated fatty acid dependent manner. Here we have
uncovered a member of the STARD family capable of regulating PPAR activity. Our
characterization of the STARD2-PPARδ interaction uncovered a previously unknown role of lipid
transport proteins in directly engaging with and repressing PPARδ activity in a ligand dependent
manner. In parallel, we have also characterized the role that gut flora play in regulating PPAR
activity. We identified a gut derived obesogen delta-valerobetaine (VB). Treatment of mice with
VB results in diet induced weight gain and hepatic steatosis. This phenotype was posited to occur
by inhibiting lipid metabolism and influencing the activity of hepatic PPARs. Here we describe
the molecular mechanism the underpins the observed phenotype and show that VB is capable of
altering carnitine biosynthesis and carnitine shuttling, effectively decreasing lipid metabolism.
Taken together we have identified two novel mechanisms by which host and microbial processes
are able to affect PPAR activity and have uncovered several new targets capable of tuning PPAR
transactivation upstream of directly modulating these receptors.
Table of Contents
PEROXISOME PROLIFERATOR
ACTIVATING RECEPTORS VIA HOST AND MICROBIAL DERIVED PROCESSES ..21
1.1 INTRODUCTION TO NUCLEAR RECEPTORS .....................................................................................21
1.2 VARIOUS LIPIDS CONTROL NR FUNCTION ....................................................................................23
1.3 PPAR FAMILY OF NUCLEAR RECEPTORS: .......................................................................................28
1.4 HOW DO PPARS ACQUIRE LIPIDS? ..................................................................................................29
1.5 LIPID TRANSFER PROTEINS ........................................................................................................................29
1.5.1 FABPs .....................................................................................................................................................31
1.6 CASE STUDIES: FABP—PPAR INTERACTION .....................................................................................34
1.6.1 FABP5—PPARδ ..................................................................................................................................34
1.6.2 FABP4—PPARγ ..................................................................................................................................34
1.6.3 FABP1— PPARα ................................................................................................................................35
1.7 STRUCTURAL INSIGHTS INTO LIGAND DRIVEN NUCLEAR IMPORT OF FABPS ............................36
1.8 GUT MICROBIOME REGULATION OF PPARS: .........................................................................................39
1.9 PPARS AND COVID-19: ............................................................................................................................41
2.10 REFERENCES ................................................................................................................................................45
CHAPTER 2: LIGAND-DEPENDENT INTERACTION BETWEEN
PHOSPHATIDYLCHOLINE TRANSFER PROTEIN AND PPARΔ: IMPLICATIONS
FOR METABOLIC SYNDROME ................................................................................................................55
2.1 SUMMARY: .....................................................................................................................................................55
THIS CHAPTER IS CURRENTLY UNDER REVIEW AT NATURE COMMUNICATIONS. ................................55
2.2 INTRODUCTION: ............................................................................................................................................57
2.3 RESULTS: ........................................................................................................................................................59
2.3.1 RNA-seq analysis of liver tissue from Pctp -/- mice ...................................................................59
2.3.2 In vivo characterization of L-Pctp-/- ..............................................................................................63
2.3.3 Defining the PC-TP – PPAR interactome; discovery of a repressive interaction
between PC-TP and PPARδ .......................................................................................................................73
2.3.4 Domain mapping of the PPARδ–PC-TP and PPARδ–FABP5 complex ............................76
2.3.5 Altered lipid levels modulate the interaction between PC-TP or FABP5 with PPARδ .79
2.4 DISCUSSION: .................................................................................................................................................85
2.5 MATERIALS AND METHODS: .....................................................................................................................90
2.6 REFERENCE: .................................................................................................................................................107
CHAPTER 3: MOLECULAR MECHANISMS OF THE GUT MICROBIOME-DERIVED
OBESOGEN DELTA-VALEROBETAINE ............................................................................................111
3.1 SUMMARY: ...................................................................................................................................................111
3.3 RESULTS: ......................................................................................................................................................115
3.3.1 Uncovering the biosynthetic pathway of valerobetaine and homocarnitne ....................115
3.3.2 BBOX catalyzes the formation of homocarnitine ....................................................................117
3.3.3 Biochemical and structural characterization of VB-BBOX complex ................................119
3.3.4 Homocarnitne can engage with enzymes to form acyl homocarntines ............................122
3.3.5 Biochemical and structural characterization of VB-CRAT complex ................................124
3.4 DISCUSSION: ................................................................................................................................................129
3.5 MATERIAL AND METHODS: ......................................................................................................................131
3.6 REFERENCES: ...............................................................................................................................................136
CHAPTER 4: DISCUSSION .........................................................................................................................138
4.1 GENERAL DISCUSSION: .............................................................................................................................138
4.2 CAN STARDS MODULATE PPAR ACTIVITY? .....................................................................................138
4.2.1 STARD2—PPARδ .............................................................................................................................141
4.2.3 STARD10–PPARa ............................................................................................................................144
4.2.4 STARD7–PPAR .................................................................................................................................144
4.2.5 StAR -PPARγ ......................................................................................................................................145
4.2.6 Other Examples .................................................................................................................................146
4.3 UTILITY OF LTPS AS DRUG TARGETS ...................................................................................................147
4.4 HOW DOES GUT MICROBIOME ALTER PPAR ACTIVITY? ..................................................................150
4.5 WHAT ROLES DO PPARS PLAY IN VIRAL INFECTIONS? ....................................................................150
4.6 CONCLUSION: ..............................................................................................................................................151
4.7 REFERENCES: ...............................................................................................................................................152
APPENDIX I: MULTIPLATFORM ANALYSES REVEAL DISTINCT DRIVERS OF
SYSTEMIC PATHOGENESIS IN ADULT VERSUS PEDIATRIC COVID-19 ....................156
AI.1 SUMMARY: .................................................................................................................................................157
AI.2 INTRODUCTION .........................................................................................................................................158
AI.3 RESULTS .....................................................................................................................................................160
AI.3.1 Integrated multiomic analyses identify proteomic alterations in coagulation and fluid
shear stress response pathways in adults with COVID-19 .............................................................161
AI.3.2 Fibrinogen mediates red blood cell aggregation under static and physiological flow
conditions .......................................................................................................................................................170
AI.3.3 Fibrinogen-mediated red blood cell aggregation induces endothelial glycocalyx
degradation ...................................................................................................................................................171
AI.3.4 Plasma from patients with COVID-19 induces increased red blood cell aggregation
...........................................................................................................................................................................178
AI.3.5 Differences in RBC membrane deformability between critically ill patients with and
without COVID-19 ......................................................................................................................................179
AI.3.5 COVID-19 plasma interacts with red blood cells to damage the endothelial
glycocalyx in a vessel size-dependent manner ....................................................................................181
AI.3.6 Indicators of endothelial damage are prominent in patients with COVID-19 .............181
AI.3.7 Multiplatform analyses of plasma from pediatric COVID-19 or MIS-C patients
suggests diverging pathophysiology from adult COVID-19 ...........................................................188
AI.4 DISCUSSION ...............................................................................................................................................204
AI.5 MATERIALS AND METHODS ...................................................................................................................209
AI .6 REFERENCES .............................................................................................................................................236
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