Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration

Abstract

One Sentence Summary: The study shows protein and metabolite pathways affected during neurodegeneration and that replenishing metabolites provides a neuroprotective effect on the retina. Abstract: 244Main Text: 9,039References: 83 AbstractNeurodegenerative diseases are debilitating, incurable disorders caused by progressive neuronal cell death.Retinitis pigmentosa (RP) is a blinding neurodegenerative disease that results in retinal photoreceptor cell death and progresses to the loss of the entire neural retinal network. We previously found that proteomic analysis of the adjacent vitreous serves as way to indirectly biopsy the neural retina and identify changes in the retinal proteome. We therefore analyzed protein expression in liquid vitreous biopsies from autosomal recessive retinitis pigmentosa (arRP) patients with PDE6A mutations and arRP mice with Pde6ɑ mutations. Proteomic analysis of retina and vitreous samples identified molecular pathways affected at the onset of photoreceptor cell death. Based on affected molecular pathways, arRP mice were treated with a ketogenic diet or metabolites involved in fatty-acid synthesis, oxidative phosphorylation, and the tricarboxylic acid (TCA) cycle. Dietary supplementation of a single metabolite, ɑ-ketoglutarate, increased docosahexaeonic acid (DHA) levels, provided neuroprotection, and enhanced visual function in arRP mice. A ketogenic diet delayed photoreceptor cell loss, while vitamin B supplementation had a limited effect. Finally, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) revealed restoration of key metabolites that correlated with our proteomic findings: pyrimidine and purine metabolism (uridine, dihydrouridine, and thymidine), glutamine and glutamate (glutamine/glutamate conversion), and succinic and aconitic acid (TCA cycle). This study demonstrates that replenishing TCA cycle metabolites via oral supplementation prolongs vision and provides a neuroprotective effect on the photoreceptor cells and inner retinal network.

Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness

“…Previous proteomic analysis of the non-diseased human vitreous by our group identified over 1,000 non-redundant intracellular proteins with diverse molecular functions ( Figure 3 B). Our research has also demonstrated that retinal, RPE, and choroidal proteins are deposited into the vitreous, and that proteomic analysis of liquid vitreous biopsies can detect molecular changes in the adjacent retina, uncover potential diagnostic biomarkers, and identify protein targets for therapy ( Skeie et al., 2015 ; Wert et al., 2020 ). This supports the concept that the vitreous is not only an ultrafiltrate of the blood but also represents its surrounding ocular tissues.…”

“…LC-MS/MS analysis revealed that synaptic signaling proteins (e.g., neurexin-2, glutamate receptor 4, neurofascin, neuronal growth regulator 1, and oligodendrocyte-myelin glycoprotein) were depleted in NIV vitreous compared with non-inflammatory controls ( Velez et al., 2019 ). It is possible that the loss of the identified synaptic signaling proteins contributes to the early ERG defect that is characteristic of NIV ( Velez et al., 2019 ; Wert et al., 2020 ). Whether CAPN5 directly targets these proteins in the retina (or their upstream effectors) is still not known.…”

“…Inherited mutations in genes result in the production of dysfunctional proteins that lead to irreversible photoreceptor damage and vision loss ( Hurley and Chao, 2020 ; Tsang et al., 2008 ). Patients with retinal dystrophy often do not display visual symptoms until a significant fraction of their photoreceptors have died, making the timing of therapeutic intervention difficult ( Wert et al., 2020 ). Furthermore, the genetic heterogeneity of these patients makes gene therapy and CRISPR-based interventions unfeasible in the near term ( DiCarlo et al., 2018 ; Takahashi et al., 2018 ; Xu et al., 2018 ).…”

“…However, the scarcity of vitreous samples from these patients prevented further evaluation of biomarker expression at different disease stages in humans. To achieve statistical power, our group analyzed vitreous and retinal protein expression in a murine model of arRP disease ( Pde6ɑ D670G mice) at early-, mid-, and late-stage disease ( Wert et al., 2020 ). We observed a significant redistribution of proteins between vitreous at early arRP, indicating that dying retinal cells had leaked proteins into the adjacent vitreous, signaling the onset of photoreceptor degeneration.…”

Apoptotic cells secrete metabolites to regulate immune homeostasis

“…Together, these findings provide proof‐of‐concept evidence that metabolites, in particular those secreted during apoptosis, can exhibit anti‐inflammatory properties in disease settings. It should be noted that the application of metabolites for therapeutic purposes is an area of growing interest, with recently reported examples including the use of microbiota‐derived metabolites in the maintenance of intestinal homeostasis, 19 and the treatment of retinal neurodegeneration with oxidative phosphorylation and tricarboxylic acid cycle metabolites 20 . Whether MeMix 3 or other combinations of metabolites found in the apoptotic cell metabolite secretome could be developed as new therapeutics for inflammatory diseases would certainly be of interest in future studies.…”