Biology subjects

Puja, A.

Publications and source records attributed to Puja, A..

6 recordsLinked to original sources

bioRxiv2026

Aging Differentially Remodels the Retina and RPE/Choroid Proteome and Metabolism

Purpose: The neural retina and retinal pigment epithelium/choroid (RPE/Cho) are metabolically coupled. Metabolic dysfunction of the RPE/Cho contributes to photoreceptor death in age-related macular degeneration (AMD). This study aimed to determine how aging, a major risk factor for AMD, alters the proteome and metabolic pathways in the retina and RPE/Cho. Methods: We performed quantitative proteomics on neural retina and RPE/Cho from young (8-week) and old (73-week) C57BL/6J mice. The differentially expressed proteins between old and young, as well as between the retina and RPE/Cho, were visualized using volcano plots and heatmaps, and functional analyses were assessed by Gene Ontology enrichment tools. Results: Aging altered the expression of 85 retinal proteins and 272 RPE/Cho, with 16 shared between tissues. In the aged retina, proteins associated with NADP(H) metabolism, neurodegeneration, and immunity were mostly upregulated, while proteins in lipid metabolism, transcription, and epigenetic regulation decreased. In the aged RPE/Cho, all 21 significantly altered lysosomal enzymes and transport proteins increased, together with complement components, and photoreceptor outer segment proteins. These changes accompanied increases in proteins associated with lipid metabolism and protection against lipid peroxidation, while several glutathione metabolism enzymes decreased. Seven shared proteins involved in lipid and NADP(H) metabolism, changed in opposite directions between retina and RPE/Cho. Comparison of the retinal and RPE/Cho proteomes identified 3073 differentially abundant proteins, of which 2452 maintained tissue-specific differences across both age groups, while approximately 17% showed age-dependent shifts in tissue enrichment. These shifts involved proteins associated with metabolism, extracellular matrix, visual function, lysosomal pathways, and innate immunity. Within the metabolic proteome, several glycolytic and fatty acid oxidation proteins showed greater relative enrichment in RPE/Cho with age, whereas glucose transporters and mitochondrial complexes shifted toward the retina. Conclusions: Overall, these findings show that aging differentially remodels the retina and RPE/Cho proteome, accompanied by altered metabolic specialization between the two tissues.

biochemistry↗

bioRxiv2026

Metabolic signatures of cone-dominant and cone-degenerating retinas

Cone photoreceptors are essential for daylight vision, and their degeneration has more profound visual consequences than rod loss in retinal degenerative diseases. Metabolic dysfunction is closely associated with cone degeneration, however the relatively small population of cones in mice and humans have limited our understanding of cone-specific metabolism. Here, we leveraged cone-dominant and cone-degeneration mouse models including Nrl-/-, Cnga3-/-, and high-dose Triiodothyronine (T3) treatment to investigate cone-specific metabolism and their metabolic impacts on the retinal pigment epithelium (RPE). Across models, cone-dominant retinas consistently showed lower pyruvate abundance alongside increases in glutathione, purines, pentose phosphate pathway intermediates, and one-carbon metabolites. Increases in several key amino acids were also associated with higher cone abundance, such as proline, arginine, alanine, valine, leucine, and hypotaurine. Strikingly, aminoadipate, an intermediate in lysine catabolism, was the most robustly changed metabolite in the retina, showing highly consistent increases across models. Relative cone increases were also associated with metabolic changes in the RPE/choroid. Like the retina, RPE/choroids showed consistent increases in aminoadipate, proline, and hypotaurine, as well as xanthosine and betaine, alongside decreases in uracil. Moreover, proteomic analysis of Nrl-/- mice showed decreases in many key metabolite transporters in the RPE/choroid, including carriers for glucose, lactate, aspartate, glutamate, serine, lysine, taurine, and proline. Collectively, these findings further our understanding of cone-specific metabolism and highlight potential cone-specific metabolic vulnerabilities in retinal degeneration.

biochemistry↗

bioRxiv2026

Early proteomic signatures of Alzheimer`s disease in the retina and brain of 3xTg-AD mice

Visual dysfunction and retinal structural alterations often precede brain pathology and cognitive decline in Alzheimers disease (AD), yet the molecular basis of these early changes and their relationship to the brain pathology remain unclear. Here, we performed quantitative proteomic profiling of retina and brain from 1-month of age triple-transgenic (3xTg-AD) mice harboring human PS1M146V, APPSwe, and tauP301L mutations, preceding detectable morphological abnormalities. Proteomic analysis identified 92 significantly altered proteins in the retina and 130 in the brain, with eight overlapping proteins between tissues. These shared proteins included three hemoglobin subunits (HBB1, HBB2, A8DUK4) and five proteins involved in metabolic regulation and intracellular transport. In addition to individual protein changes, pathway analysis demonstrated that mitochondrial metabolism and intracellular transport were commonly dysregulated in both tissues. Brain proteome was characterized by broad changes in mitochondrial-associated proteins, including respiratory chain components and mitochondrial ribosomal subunits, as well as proteins related to autophagy and synaptic vesicle pathways. In contrast, the retinal proteome was characterized by downregulation of vision-related proteins, altered small molecule transporters, and a marked reduction of the mitochondrial enzyme succinate-CoA ligase subunit {beta} (SUCB2). As SUCB2 links mitochondrial metabolism to epigenetic regulation through succinylation and lactylation, its depletion may promote mitochondria-to-nucleus signaling and early transcriptional reprogramming in the AD retina. Together, these findings demonstrate early metabolic and transport dysregulation in both retina and brain and highlight selective alterations of visual proteins in the retina. These early retinal proteomic changes provide valuable insight into understanding early metabolic disturbances in the eye and brain for AD detection.

biochemistry↗

bioRxiv2025

Absolute quantification of TCA cycle intermediates in mouse ocular tissues reveals distinct tissue- and sex-specific mitochondrial metabolism

ObjectiveMitochondrial tricarboxylic acid (TCA) cycle is central to energy production and redox balance in the eye, which must sustain high metabolic activity to support vision. Retinal neurons, the retinal pigment epithelium (RPE), cornea, and lens each have distinct physiological roles and metabolic demands, yet the absolute concentrations of key TCA intermediates and their variation by tissue, sex, and time of day are not well-defined. MethodsTargeted gas chromatography-mass spectrometry was employed to quantify the absolute concentrations of TCA cycle metabolites in mouse ocular tissues collected at 10 AM and 2 PM to capture diurnal variations. Key metabolite ratios were subsequently calculated to provide insight into TCA cycle dynamics across eye tissues. ResultsThe retina showed the highest concentrations of TCA metabolites among all ocular tissues, particularly succinate, citrate, and malate, consistent with its high energy demands. The RPE/choroid demonstrated well-balanced intermediates with the highest -ketoglutarate (-KG)/Isocitrate ratio, reflecting its efficient mitochondrial oxidation and reductive carboxylation. Corneal metabolism was featured by dominant malate, especially in females, suggesting a metabolic adaptation for redox regulation and oxidative stress defense. The lens had uniformly low metabolite levels except for succinate, indicating minimal mitochondrial activity under physiologically low oxygen conditions. Notably, both the cornea and lens showed significant sex-dependent and diurnal variations in TCA cycle intermediates. ConclusionThis study demonstrates distinct tissue-specific mitochondrial metabolism in the eye, reflecting the unique functional and biochemical demands of each tissue. These metabolic signatures may underlie their susceptibility to mitochondrial dysfunction in various ocular diseases.

biochemistry↗

bioRxiv2025

Beyond Ornithine Metabolism in Gyrate Atrophy: Tissue-Specific Proteomic Insights into Neonatal and Adult OAT Deficiency

Ornithine aminotransferase (OAT) links the urea cycle, TCA cycle, and amino acid metabolism by interconverting ornithine to pyrroline-5-carboxylate and glutamate. Mutations in OAT cause hyperornithinemia and predominantly affect the eye, leading to gyrate atrophy of the choroid and retina (GA), a rare inherited blinding disorder. To understand the early molecular changes that make the eye susceptible to damage, we performed quantitative proteomic and metabolomic profiling of liver, retina, and retinal pigment epithelium and choroid (RPE/Cho) from OAT-deficient (Oatrhg) mice prior to detectable vision impairment. In addition to reduced OAT expression and elevated ornithine, methylation-related metabolites such as N(6)-methyl-lysine were altered in all examined tissues of Oatrhgmice. In the liver, ornithine disposal through the urea cycle was enhanced, together with altered expression of detoxification enzymes and histone H2B proteins. In contrast, the retina had minimal proteomic changes but pronounced alterations in amino acid pathways supporting glutamate homeostasis. The RPE/Cho demonstrated the most extensive proteomic changes, particularly in mitochondrial metabolism, cytoskeleton, and extracellular matrix, along with reductions in metabolites involved energy metabolism and antioxidant capacity. Together, these findings highlight common and tissue-specific impacts of OAT on the liver and ocular tissues and provide insight into early molecular changes that contribute to the selective vulnerability of the eye in GA. Proteomics data are available via ProteomeXchange (PXD063614) and metabolomics data via MassIVE repository (MSV000101103).

biochemistry↗

bioRxiv2025

Gene Therapy Rescues Cone Function in an All-cone Retina Mouse Model for Blue Cone Monochromacy with the Most Common C203R Missense Mutation

Blue cone monochromacy (BCM) is an X-linked cone dystrophy characterized by loss of long- (L) and medium-wavelength (M) cone function. A common cause is the C203R missense mutation, which occurs in both OPN1LW and OPN1MW, or in hybrid OPN1LW/OPN1MW opsin genes. Because BCM primarily affects foveal cones, we generated Opn1mwC198R/Opn1sw-/-/Nrl-/- (C198RAC) mice carrying the murine equivalent of the human C203R mutation on an all-cone retinal background. C198RAC mice exhibited absent photopic ERG responses and significantly shortened cone outer segments, recapitulating foveal cone deficits in BCM. Metabolomic profiling further revealed altered retinal metabolism, including reduced cGMP and elevated oxidative stress-related metabolites. To evaluate therapy, we delivered AAV8-Y733F expressing human L-opsin (OPN1LW) cDNA under the cone-specific PR2.1 promoter at 1 and 5 months of age. Treatment restored cone function, regenerated outer segment structures, and provided rescue for at least 5 months post-injection in both early- and late-treatment groups. These results demonstrate that densely packed cones expressing only the C198R mutant opsin remain viable targets for gene therapy. Together, this study establishes the C198RAC mouse as a cone-rich model of BCM and provides compelling preclinical evidence that AAV-mediated gene augmentation can restore cone structure and function, supporting the feasibility of gene therapy for BCM.

molecular biology↗