Abstract
Altered protein levels in the aqueous humor (AH) may be a valuable source of novel biomarkers in neurodegenerative retinal disease. The proximity of this body fluid to the disease focus, and its corresponding enrichment for tissue specific proteins, renders it an excellent matrix to study underlying molecular mechanisms. Novel proteomic methods accordingly hold large potential for insight into pathologies based on the composition of the AH proteome, including primary open angle glaucoma (POAG). Recent mass spectrometry-based studies use novel approaches to tackle the challenges arising from the combination of low available sample volume and protein concentration, thereby increasing proteome coverage. But despite significant improvements in mass spectrometry (MS), a different class of proteomic technologies is poised to majorly impact the analysis of ocular biofluids. Affinity proteomic workflows, having become available commercially recently, have started to complement data obtained by MS and likely will grow into a crucial tool for ophthalmological biomarker research. This review highlights corresponding approaches in proteome analysis of aqueous humor and discusses recent findings on alterations of the AH proteome in POAG.
Introduction
The aqueous humor (AH) is an ocular fluid supplying cells and tissues of the anterior chamber with nutrients. It is produced by the ciliary epithelium and drained via the trabecular meshwork (TM) and Schlemm’s channel. AH liquid biopsies are frequently performed during surgical intervention such as trabeculectomy or cataract surgery. The liquid may, however, also be safely obtained using hydro-dissection cannulas, enabling routine sampling (). AH contains a large number of proteins specific to ocular tissue and is thus exquisitely suited to screen for molecular changes in the eye. Despite being separated from blood by the blood-aqueous-barrier (BAB), proteins typically expressed in other organs may also be found in the AH (; Yavrum et al., 2021; Wolf et al., 2023). This fact increasingly directs attention toward the AH proteome in the context of clinical biomarker research. Additionally, AH proteomics offers insight into the pathophysiology of neurodegenerative retinal disease. This review summarizes current advances in AH proteome investigation and their relevance to primary open angle glaucoma (POAG), as well as introduces relevant methodology.
Deciphering the AH proteome
Aqueous humor is collected in limited volumes of ∼50–150 μL per sampling with low protein concentrations of 0.1–0.6 μg/mL (; ; ; Nikhalashree et al., 2019). This low protein yield renders proteomic analysis of AH challenging. Additionally, a high dynamic range of protein concentrations in AH (7 orders of magnitude), implies challenges similar to those faced in plasma proteomics (Yu et al., 2020). In AH, just 17 proteins constitute two thirds of the total protein content, with albumin alone accounting for approximately 37% (Figure 1). The remaining third again is dominated by 27 medium abundance proteins and low abundant proteins only represent 1% of the total (Yu et al., 2020). This protein concentration challenge is frequently tackled using depletion of high abundant proteins to enable detection of low abundance components (). Functionally, AH proteins are mainly involved in immune response, inflammation, coagulation as well as energy metabolism (Yu et al., 2020), and it is considered strongly influenced by sex and ethnicity (Perumal et al., 2017; ; Vashishtha et al., 2023). General challenges in ocular liquid proteomics have recently been reviewed (Wolf et al., 2024).
FIGURE 1
Although AH may be safely sampled via paracentesis (
Current data bases cataloging the AH proteome contain 827 to 1,888 proteins identified using MS. Prominent resources are the EyeOme project under the auspices of the human proteome organization (HUPO) (
Although 2D-LC-MS/MS shotgun proteomics delivered good results in identifying 800+ protein groups in AH (Yu et al., 2020; Liu X. et al., 2021), data-independent acquisition (DIA) is increasingly applied in clinical proteomics and slowly replaces the more traditional data-dependent acquisition (DDA) approaches (
Mass spectrometry (MS)-based AH proteomics, offering untargeted protein identification and high specificity, represents an outstanding asset. Achieving comprehensive protein coverage, however, commonly necessitates the depletion of high-abundant proteins and sample pre-fractionation. Consequently, and due to co-depletion, loss through surface coating in complex workflows and similar effects, detection of biomarkers in the low-abundant ranges is rendered challenging and inefficient.
The protein coverage of modern affinity-based assay platforms thus currently outperforms the analytical depth of state-of-the-art MS workflows in complex body fluids by a wide margin. Novel affinity proteomics discovery platforms, such as SomaScan 11k and Olink Explore HT, enable the analysis of thousands of protein targets in a semi-quantitative manner—without any sample pre-processing. While being largely developed for the analysis of blood-derived samples, the platforms offer access to sample matrices beyond those, including saliva (Scholtz et al., 2020), urine (
As suggested by its moniker, the new SomaScan 11K platform, developed by Somalogic, provides ∼11,000 protein targets, encompassing half the human proteome, and provides the deepest coverage of all currently available methods (SomaLogic, 2024). For protein binders, SomaScan utilizes enhanced aptamers, short oligo single strand DNA (ssDNA) nucleotides, named slow off-rate modified aptamers (SOMAmers). Chemically modified to enhance affinity to protein targets, SOMAmers are conjugated to a fluorophore and a biotin tag via a photocleavable linker. Bound to streptavidin beads they capture proteins from the sample. Following biotinylation of captured proteins and cleavage of SOMAmer/protein complexes from the beads using UV light, the complexes are recaptured on fresh beads via the biotinylated proteins and SOMAmers eluted and analyzed on a microarray chip with signal intensity correlating to protein concentration. A first study using the SomaScan platform for ocular fluid analysis was conducted by Pessuti et al. (2023). AH from 28 patients with infectious uveitis and 29 samples from non-infectious uveitis patients was analyzed in comparison to 35 AH samples from cataract patients, using the SomaScan v3 Assay, identifying a minimum of 4,074 proteins across all groups.
An updated version of the SomaScan assay (v4.1) comprising 6,345 protein targets was also recently applied to analyze AH and VH liquid biopsies (Wolf et al., 2023). The authors were able to detect 5,953 proteins in the AH of healthy subjects, 5,887 of which replicated paired RNA-seq findings. This represents a significant improvement in analysis depth as compared to existing LC-MS/MS approaches. It is noteworthy, that the target menu of SomaScan v4.1 lacks coverage of various eye specific targets (Wolf et al., 2024), rendering likely an even higher number of protein detections from the sample type when subjected to the novel 11k panel.
A strong competitor in large panel affinity proteomics is the Swedish company Olink. Its Olink Explore HT platform covers approximately 5,400 protein targets and is based on proximity extension assay (PEA) technology (Olink, 2024). PEA uses two antibodies binding to distinct epitopes on a target protein. The antibodies covalently carry DNA probes that hybridize when in proximity. PCR amplifies the double-stranded sequences for readout using qPCR or Next-Gen Sequencing. Target protein-specific DNA barcodes comprised within the amplicon correlate with protein concentration, enabling relative protein abundance measurements. PEA offers minimal cross-reactivity, as well as high specificity and multiplexing capacity across a broad dynamic range, rendering it ideal for high-throughput analyses. While the latest Explore HT platform has yet to be applied to AH proteomics, the method has proven applicable using smaller panels and shown good detectability of AH proteins, as ∼70% of proteins form different Olink Target panels were detected in at least 30% of patients (Wilson et al., 2023). Olink affinity proteomic data from AH liquid biopsies was further demonstrated to be valuable for the prognosis of metastasis in uveal melanoma, an intraocular malignancy, rendering disease state accessible even in the absence of tumor biopsies (Wierenga et al., 2019; Peng et al., 2023). Here both the Olink Target Immuno-Oncology panel, targeting 90 marker proteins (Wierenga et al., 2019), as well as the more comprehensive Explore 1.5k panel, covering ∼1,500 protein targets (Peng et al., 2023) where employed to analyze AH samples. The studies identified new potential biomarkers for disease prognosis as well as stratification of metastasis, and highlight the efficacy of PEA-based methodology to comprehensively profile the AH proteome for biomarker discovery and mechanistic insight into the underlying disease.
Correlation of serum and AH proteins: crossing the blood-aqueous-barrier?
Even though sampling of AH via paracentesis is considered safe (
Another promising sample source for analyzing disease related proteome alterations and gaining insight into molecular disease mechanisms is the VH. Its proximity to the retina and optic nerve head renders it appealing for proteomic analysis. Unfortunately, obtaining samples of VH carries a significant risk for complications, resulting in limited availability for clinical studies. In contrast to limited exchange with blood via the BAB, however, studies have demonstrated the diffusion of vitreous proteins into the AH, alongside a significant correlation between the proteomic profiles of AH and VH (Wu et al., 2020; Wilson et al., 2023). In extension of that work it was only recently demonstrated that 87% of VH proteins were also detected in AH (Wolf et al., 2023). This provides an opportunity to examine differential protein expression linked to pathological changes in both the anterior and posterior portions of the eye through AH, thus potentially rendering accessible indicators of retinal neurodegeneration.
Novel insight into glaucomatous changes of the aqueous humor proteome
Glaucoma is an umbrella term for a variety of conditions with a heterogenous presentation. They have in common a characteristic loss of retinal ganglion cells (RGCs) and associated optic nerve damage. Elevated intraocular pressure (IOP) is strongly correlated with, but not solely causative of glaucoma (Leske et al., 2001;
In primary open-angle glaucoma (POAG), AH efflux is impaired by enhanced extracellular matrix (ECM) deposition and altered actin cytoskeleton dynamics, causing a stiffening of TM tissue. In contrast, AH drainage in pseudoexfoliation glaucoma (PEXG) is obstructed by an accumulation of pseudoexfoliation material. Although different root causes may increase AH outflow resistance, they share the outcome of dysregulated AH dynamics. Frequent reports of AH proteome alteration associated with glaucoma underscore the significant role of AH dynamics in this disease and the analysis of its proteome consequently attractive to exploration of molecular mechanisms and identification of candidate drug targets.
A higher total protein concentration of AH in POAG has been reported repeatedly (Nikhalashree et al., 2019;
Currently, MS-based workflows represent the vanguard of AH proteomics. An overview of recent POAG studies on the AH proteome is given in Table 1. The highest protein coverage in a single experiment comparing proteomes of POAG and control samples, was accomplished to date by
TABLE 1
| Goal of investigation | Samples (n) | Method details | Protein IDs | References | |
| Machine | Method | ||||
| Complement proteins in POAG | 258 (196 CAT, 62 POAG) | Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) | LC-MS/MS, DDA | 32 | Vashishtha et al., 2023 |
| Pathological processes and biomarker candidates | 10 (5 POAG vs. 5 CTRL) | QExactive MS (Thermo Scientific) Easy-nLC nano-LC (Thermo Scientific) | LC-MS/MS, DDA, HRM-MS (SWATH) | 448 | |
| Proteome changes in POAG and PACG | 9 (3 POAG, 3 PACG, 3 CAT) | NA | LC-MS/MS, MSe mode | 184 CAT 190 POAG 299 PACG | Nikhalashree et al., 2019 |
| Exosomes in AH: sub-proteome | 26 (16 POAG, 10 CTRL) | QExactive MS (Thermo Scientific) Easy-nLC nano-LC (Thermo Scientific) | iTRAQ (8-plex) | 15 | Mueller et al., 2023 |
| POAG related proteomic changes | 35 (12 CAT, 23 POAG) | Linear trap quadrupole Orbitrap MS | LC-MS/MS | 175 | Liu et al., 2020 |
| Explore pathogenesis, Identify drug targets | 20 (10 POAG, 10 CAT) | QExactive MS (Thermo Scientific) | Nano-HPLC-MS, LFQ | 610 | Liu A. et al., 2021 |
| Correlation of AH proteome with visual field indices | 49 (POAG only) | Orbitrap Fusion Tribrid (Thermo Scientific) Ultimate 3000 nano-UPLC (Thermo Scientific) | DDA LC-MS/MS | 222 | |
| AH proteome glaucoma with and without PEX | 29 (13 POAG (6/w PEX, 7/wo PEX) vs. 16 CAT (5/w PEX, 11/wo PEX)) | Orbitrap QExactive (Thermo Scientific) | LFQ, DDA | 269 | |
| POAG pathogenesis and progression, treatment effects | 10 (5 POAG, 5 CAT) | LFQ: QExactive (Thermo Fisher, Waltham, MA, USA) Dionex UltiMate 3000 UHPLC; MRM: TSQ Vantage triple quadrupole + EASY-nLC nano-LC (Thermo Scientific) | LC-MS/MS, LFQ, +MRM-MS | 865 | |
| Proteomic alterations in POAG | 47 (32 CAT, 15 POAG) | Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) Ultimate 3000 nano-UPLC (Thermo Scientific) | LC-MS/MS | 401 | Sharma et al., 2018 |
Overview of recent AH proteome studies in POAG.
HRM, hyper reaction monitoring; CAT, cataract; POAG, primary open angle glaucoma; PACG, primary angle closure glaucoma; CTRL, control; PEX, pseudoexfoliation; DDA, data-dependent acquisition; DIA, data-independent acquisition; SWATH-MS, sequential window acquisition of all theoretical mass spectra; iTRAQ, isobaric tags for relative and absolute quantitation.
Another protein class frequently linked to eye disease by proteomics is that of apolipoproteins. Apolipoprotein D (APOD), in particular, is found upregulated in AH of POAG patients (
Beyond the frequently observed alteration in apolipoproteins and the complement cascade, various other glaucoma pathogenesis associated proteins were identified in AH. An accumulation of amyloid-beta (Aβ), associated with Alzheimer’s disease (
Furthermore, with GSTP1, a protein involved in the glutathione metabolism pathway associated with increased reactive oxygen species production and oxidative stress was identified as reduced in AH of POAG patients with cataract, (Liu A. et al., 2021). Low GSTP1 levels were discovered by MS-based proteomic analysis and subsequently verified by enzyme-linked immunosorbent assay (ELISA), validating this potential biomarker candidate and new treatment target. The authors identified a further 48 up- and 49 downregulated proteins in POAG that were mainly involved in the processes of inflammation, oxidative stress and ECM remodeling. These changes in oxidative stress response and inflammation are hypothesized to be linked to pathogenic alterations in the AH microenvironment. Other proteins associated with glycosylation, immune response, molecular transport and lipid metabolism (especially cholesterol homeostasis), such as NPC2, COL18A1, SERPINF2, NWD1 and KIAA0100, were found to be correlated with POAG odds ratios (Sharma et al., 2018). Receiver operating characteristic (ROC) analysis of these proteins further revealed promising potential for use as diagnostic biomarkers (AUC = 0.751 – AUC = 0.793).
Not only the liquid phase of AH is subject to disease related alterations, but cargo of AH derived extracellular vesicles (EVs) also differ between POAG and controls (Mueller et al., 2023). EV proteins from POAG patients and controls were labeled using isobaric tags for relative and absolute quantitation (iTRAQ) (Ross et al., 2004;
Conclusion
State-of-the-art MS proteomic workflows are increasingly expanding the knowledge about the AH proteome in health and disease. Several identified differentially expressed proteins bear the potential to serve as disease biomarkers in AH-based diagnostics. A transition from AH biomarkers to detection in blood-based samples, however, does not appear realizable as correlation between the two matrices proves insufficient. While sampling of AH is considered safe, it remains uncomfortable and is thus unlikely to be suitable for standard diagnostic testing. However, AH proteome studies shine in the discovery of disease mechanisms, with application in the development of causative treatments or neuroprotection through identification of candidate drug targets. Large potential for furthering such mechanistic insight from AH-analysis in glaucoma research lies with novel affinity proteomic technologies, which largely remain underutilized. The astounding capacity of such platforms to provide extensive protein coverage under conditions of extreme dynamic protein concentration range and using minimal amounts of precious sample material at high throughput is expected to significantly advance the field in the years to come.
Statements
Author contributions
VB: Conceptualization, Visualization, Writing – original draft, Writing – review & editing. JG: Conceptualization, Funding acquisition, Supervision, Writing – review & editing.
Funding
The authors declare that no financial support was received for the research, authorship, and/or publication of this article.
Conflict of interest
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Summary
Keywords
aqueous humor (AH), proteomics, affinity proteomics, primary open angle glaucoma (POAG), biomarkers, LC-MS/MS, SOMAmer, proximity extension assay (PEA)
Citation
Beutgen VM and Graumann J (2024) Advances in aqueous humor proteomics for biomarker discovery and disease mechanisms exploration: a spotlight on primary open angle glaucoma. Front. Mol. Neurosci. 17:1397461. doi: 10.3389/fnmol.2024.1397461
Received
07 March 2024
Accepted
10 April 2024
Published
24 April 2024
Volume
17 - 2024
Edited by
Steven J. Pittler, University of Alabama at Birmingham, United States
Reviewed by
Michael Farkas, University at Buffalo, United States
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Copyright
© 2024 Beutgen and Graumann.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Vanessa M. Beutgen, vanessa.beutgen@uni-marburg.deJohannes Graumann, johannes.graumann@uni-marburg.de
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