Tag Archives: CMP

Unbalanced Redox Status Network As An Early Pathological Event In Congenital Cataracts

We have a new manuscript from the lab in Experimental Eye Research, (PubMed link here). Metabolic changes and retinal remodeling in Heterozygous CRX mutant cats (CRXRDY/+). This manuscript is in collaboration with the Sheldon Rowan lab out of Tufts University.  Authors are: Eloy Bejarano, Elizabeth A Whitcomb, Rebecca L Pfeiffer (@BeccaPfeiffer19), Kristie L Rose, Maria José Asensio, José Antonio Rodríguez-Navarro, Alejandro Ponce-Mora, Antolín Canto, Inma Almansa, Kevin L Schey, Bryan W Jones (@BWJones), Allen Taylor, and Sheldon Rowan (@SheldonRowan). The PDF is here.

Abstract: The lens proteome undergoes dramatic composition changes during development and maturation. A defective developmental process leads to congenital cataracts that account for about 30% of cases of childhood blindness. Gene mutations are associated with approximately 50% of early-onset forms of lens opacity, with the remainder being of unknown etiology. To gain a better understanding of cataractogenesis, we utilized a transgenic mouse model expressing a mutant ubiquitin protein in the lens (K6W-Ub) that recapitulates most of the early pathological changes seen in human congenital cataracts. We performed mass spectrometry-based tandem-mass-tag quantitative proteomics in E15, P1, and P30 control or K6W-Ub lenses. Our analysis identified targets that are required for early normal differentiation steps and altered in cataractous lenses, particularly metabolic pathways involving glutathione and amino acids. Computational molecular phenotyping revealed that glutathione and taurine were spatially altered in the K6W-Ub cataractous lens. High-performance liquid chromatography revealed that both taurine and the ratio of reduced glutathione to oxidized glutathione, two indicators of redox status, were differentially compromised in lens biology. In sum, our research documents that dynamic proteome changes in a mouse model of congenital cataracts impact redox biology in lens. Our findings shed light on the molecular mechanisms associated with congenital cataracts and point out that unbalanced redox status due to reduced levels of taurine and glutathione, metabolites already linked to age-related cataract, could be a major underlying mechanism behind lens opacities that appear early in life.

Metabolic changes and retinal remodeling in Heterozygous CRX mutant cats (CRXRDY/+)

We have a new manuscript from the lab in Experimental Eye Research, (PubMed link here). Metabolic changes and retinal remodeling in Heterozygous CRX mutant cats (CRXRDY/+). This manuscript is in collaboration with the Simon Petersen-Jones lab out of Michigan State University.  Authors are: Laurence M. Occelli, Bryan W. Jones @BWJones, Taylor J. Cervantes, and Simon M. Petersen-Jones. The PDF is here.

Abstract: CRX is a transcription factor essential for normal photoreceptor development and survival. The CRXRdy cat has a naturally occurring truncating mutation in CRX and is a large animal model for dominant Leber congenital amaurosis. This study investigated retinal remodeling that occurs as photoreceptors degenerate. CRXRdy/+ cats from 6 weeks to 10 years of age were investigated. In vivo structural changes of retinas were analyzed by fundus examination, confocal scanning laser ophthalmoscopy and spectral domain optical coherence tomography. Histologic analyses including immunohistochemistry for computational molecular phenotyping with macromolecules and small molecules. Affected cats had a cone-led photoreceptor degeneration starting in the area centralis. Initially there was preservation of inner retinal cells such as bipolar, amacrine and horizontal cells but with time migration of the deafferented neurons occurred. Early in the process of degeneration glial activation occurs ultimately resulting in formation of a glial seal. With progression the macula-equivalent area centralis developed severe atrophy including loss of retinal pigmentary epithelium. Microneuroma formation occurs in advanced stages as more marked retinal remodeling occurred. This study indicates that retinal degeneration in the CrxRdy/+ cat retina follows the progressive, phased revision of retina that have been previously described for retinal remodeling. These findings suggest that therapy dependent on targeting inner retinal cells may be useful in young adults with preserved inner retinas prior to advanced stages of retinal remodeling and neuronal cell loss.

Pathoconnectome Analysis of Müller Cells in Early Retinal Remodeling

We have a new manuscript out in Clinical Neurophysiology, An Update on Retinal Prostheses. PubMedDirect Link PDF here.

Authors: Rebecca L Pfeiffer, James R Anderson, Daniel P Emrich, Jeebika Dahal, Crystal L Sigulinsky, Hope AB Morrison, Jia-Hui Yang, Carl B Watt, Kevin D Rapp, Mineo Kondo, Hiroko Terasaki, Jessica C Garcia, Robert E Marc, and Bryan W Jones.

Abstract: Glia play important roles in neural function, including but not limited to amino acid recycling, ion homeostasis, glucose metabolism, and waste removal. During retinal degeneration and subsequent retinal remodeling, Müller cells (MCs) are the first cells to show metabolic and morphological alterations in response to stress. Metabolic alterations in MCs chaotically progress in retina undergoing photoreceptor degeneration; however, what relationship these alterations have with neuronal stress, synapse maintenance, or glia-glia interactions is currently unknown. The work described here reconstructs a MC from a pathoconnectome of early retinalremodeling retinalpathoconnectome 1 (RPC1) and explores relationships between MC structural and metabolic phenotypes in the context of neighboring neurons and glia. Here we find variations in intensity of osmication inter- and intracellularly, variation in small molecule metabolic content of MCs, as well as morphological alterations of glial endfeet. RPC1 provides a framework to analyze these relationships in early retinal remodeling through ultrastructural reconstructions of both neurons and glia. These reconstructions, informed by quantitative metabolite labeling via computational molecular phenotyping (CMP), allow us to evaluate neural-glial interactions in early retinal degeneration with unprecedented resolution and sensitivity.



Retinal Remodeling And Metabolic Alterations in Human AMD

We have a new publication out (direct link, open access), Müller Cell Metabolic Chaos During Retinal Degeneration authored by Bryan W. JonesRebecca Pfeiffer, William Ferrell, Carl Watt, James Tucker, and Robert Marc.


Age-related macular degeneration (AMD) is a progressive retinal degeneration resulting in central visual field loss, ultimately causing debilitating blindness. AMD affects 18% of Americans from 65 to 74, 30% older than 74 years of age and is the leading cause of severe vision loss and blindness in Western populations. While many genetic and environmental risk factors are known for AMD, we currently know less about the mechanisms mediating disease progression. The pathways and mechanisms through which genetic and non-genetic risk factors modulate development of AMD pathogenesis remain largely unexplored. Moreover, current treatment for AMD is palliative and limited to wet/exudative forms. Retina is a complex, heterocellular tissue and most retinal cell classes are impacted or altered in AMD. Defining disease and stage-specific cytoarchitectural and metabolic responses in AMD is critical for highlighting targets for intervention. The goal of this article is to illustrate cell types impacted in AMD and demonstrate the implications of those changes, likely beginning in the retinal pigment epithelium (RPE), for remodeling of the the neural retina. Tracking heterocellular responses in disease progression is best achieved with computational molecular phenotyping (CMP), a tool that enables acquisition of a small molecule fingerprint for every cell in the retina. CMP uncovered critical cellular and molecular pathologies (remodeling and reprogramming) in progressive retinal degenerations such as retinitis pigmentosa (RP). We now applied these approaches to normal human and AMD tissues mapping progression of cellular and molecular changes in AMD retinas, including late-stage forms of the disease.

Müller Cell Metabolic Chaos During Retinal Degeneration

We have a new publication out (direct link, open access), Müller Cell Metabolic Chaos During Retinal Degeneration authored by Rebecca PfeifferRobert Marc, Mineo Kondo, Hiroko Terasaki and Bryan W. Jones.


Müller cells play a critical role in retinal metabolism and are among the first cells to demonstrate metabolic changes in retinal stress or disease. The timing, extent, regulation, and impacts of these changes are not yet known. We evaluated metabolic phenotypes of Müller cells in the degenerating retina.

Retinas harvested from wild-type (WT) and rhodopsin Tg P347L rabbits were fixed in mixed aldehydes and resin embedded for computational molecular phenotyping (CMP). CMP facilitates small molecule fingerprinting of every cell in the retina, allowing evaluation of metabolite levels in single cells.

CMP revealed signature variations in metabolite levels across Müller cells from TgP347L retina. In brief, neighboring Müller cells demonstrated variability in taurine, glutamate, glutamine, glutathione, glutamine synthetase (GS), and CRALBP. This variability showed no correlation across metabolites, implying the changes are functionally chaotic rather than simply heterogeneous. The inability of any clustering algorithm to classify Müller cell as a single class in the TgP347L retina is a formal proof of metabolic variability in the present in degenerating retina.

Although retinal degeneration is certainly the trigger, Müller cell metabolic alterations are not a coherent response to the microenvironment. And while GS is believed to be the primary enzyme responsible for the conversion of glutamate to glutamine in the retina, alternative pathways appear to be unmasked in degenerating retina. Somehow, long term remodeling involves loss of Müller cell coordination and identity, which has negative implications for therapeutic interventions that target neurons alone.

Retinal Remodeling in Human Retinitis Pigmentosa

We have a new publication out (Direct Link, Free Open Access), Retinal Remodeling in Human Retinitis Pigmentosa authored by Bryan W. Jones, Rebecca Pfeiffer, Drew Ferrell, Carl Watt, Michael Marmor and Robert Marc.

Abstract: Retinitis Pigmentosa (RP) in the human is a progressive, currently irreversible neural degenerative disease usually caused by gene defects that disrupt the function or architecture of the photoreceptors. While RP can initially be a disease of photoreceptors, there is increasing evidence that the inner retina becomes progressively disorganized as the outer retina degenerates. These alterations have been extensively described in animal models, but remodeling in humans has not been as well characterized. This study, using computational molecular phenotyping (CMP) seeks to advance our understanding of the retinal remodeling process in humans. We describe cone mediated preservation of overall topology, retinal reprogramming in the earliest stages of the disease in retinal bipolar cells, and alterations in both small molecule and protein signatures of neurons and glia. Furthermore, while Müller glia appear to be some of the last cells left in the degenerate retina, they are also one of the first cell classes in the neural retina to respond to stress which may reveal mechanisms related to remodeling and cell death in other retinal cell classes. Also fundamentally important is the finding that retinal network topologies are altered. Our results suggest interventions that presume substantial preservation of the neural retina will likely fail in late stages of the disease. Even early intervention offers no guarantee that the interventions will be immune to progressive remodeling. Fundamental work in the biology and mechanisms of disease progression are needed to support vision rescue strategies.

In Situ Metabolomic Signatures Of Neuroprotection, Apoptosis, And Microglial Phagocytosis

This abstract was presented July 1st at the 11th International Converence of the Metabolomics Society at the University of California, Davis by Felix Vazquez-Chona, Drew Ferrell, Bryan W. Jones and Robert E. Marc.


Metabolic dysregulation is an early hallmark of neurodegenerative diseases including Alzheimer’s disease and age-related macular degeneration. Mapping metabolic adaptation with cellular resolution and tissue- wide context is crucial to define networks regulating neuronal survival, cell death progression, and immune cell response.

Computational Molecular Phenotyping (CMP) explores the amine metabolome (amino acids and amines). Technically, CMP metabolomics combines amine metabolite trapping, ultrathin microscopy (50-200 nm), immunodetection, pattern recognition, and clustering algorithms. Here we mapped the in situ distribution of over 30 core amine metabolites in retinal cells challenged by light-induced oxidative stress. Metabolomic profiles were phenotyped using ultrastructural, biochemical, and proteomic indices of oxidative stress.

CMP enabled precise visualization of >30 metabolites in every retinal cell. CMP resolved and phenotyped metabolomic profiles to specific degeneration and microglial functional states in the light-damaged retina. Cone photoreceptor survival correlated with enhanced antioxidant glutathione content. Rod photoreceptor apoptosis coincided with rapid depletion of organic osmolytes followed by nuclear import of cationic arginine metabolites. Delay in cell death increased necrosis and DNA damage-induced apoptosis. Microglial chemotaxis enhanced distinct signatures of glutamate and glutathione metabolism; whereas, phagocytosis coinduced classic (M1) and alternative (M2) arginine metabolites of macrophage activation.

CMP discovers and phenotypes cell classes, tracks cell state, and maps disease with single-cell resolution in any tissue or organism.