Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma

BACKGROUND

Class 2 uveal melanomas are associated with the inactivation of the BRCA1 ((breast cancer type 1 susceptibility protein)-associated protein 1 (BAP1)) gene. Inactivation of BAP1 promotes the upregulation of vitamin K-dependent protein S (PROS1), which interacts with the tyrosine-protein kinase Mer (MERTK) receptor on M2 macrophages to induce an immunosuppressive environment.

METHODS

We simulated the interaction of PROS1 with MERTK with ColabFold. We evaluated PROS1 and MERTK for the presence of intrinsically disordered protein regions (IDPRs) and disorder-to-order (DOT) regions to understand their protein-protein interaction (PPI). We first evaluated the structure of each protein with AlphaFold. We then analyzed specific sequence-based features of the PROS1 and MERTK with a suite of bioinformatics tools.

RESULTS

With high-resolution, moderate confidence, we successfully modeled the interaction between PROS1 and MERTK (predicted local distance difference test score (pDLLT) = 70.68). Our structural analysis qualitatively demonstrated IDPRs (i.e., spaghetti-like entities) in PROS1 and MERK. PROS1 was 23.37 % disordered, and MERTK was 23.09 % disordered, classifying them as moderately disordered and flexible proteins. PROS1 was significantly enriched in cysteine, the most order-promoting residue (p-value <0.05). Our IUPred analysis demonstrated that there are two disorder-to-order transition (DOT) regions in PROS1. MERTK was significantly enriched in proline, the most disorder-promoting residue (p-value <0.05), but did not contain DOT regions. Our STRING analysis demonstrated that the PPI network between PROS1 and MERTK is more complex than their assumed one-to-one binding (p-value <2.0 × 10-6).

CONCLUSION

Our findings present a novel prediction for the interaction between PROS1 and MERTK. Our findings show that PROS1 and MERTK contain elements of intrinsic disorder. PROS1 has two DOT regions that are attractive immunotherapy targets. We recommend that IDPRs and DOT regions found in PROS1 and MERTK should be considered when developing immunotherapies targeting this PPI.

Intrinsic disorder in PRAME and its role in uveal melanoma

INTRODUCTION

The PReferentially expressed Antigen in MElanoma (PRAME) protein has been shown to be an independent biomarker for increased risk of metastasis in Class 1 uveal melanomas (UM). Intrinsically disordered proteins and regions of proteins (IDPs/IDPRs) are proteins that do not have a well-defined three-dimensional structure and have been linked to neoplastic development. Our study aimed to evaluate the presence of intrinsic disorder in PRAME and the role these structureless regions have in PRAME( +) Class 1 UM.

METHODS

A bioinformatics study to characterize PRAME's propensity for the intrinsic disorder. We first used the AlphaFold tool to qualitatively assess the protein structure of PRAME. Then we used the Compositional Profiler and a set of per-residue intrinsic disorder predictors to quantify the intrinsic disorder. The Database of Disordered Protein Prediction (D2P2) platform, IUPred, FuzDrop, fIDPnn, AUCpred, SPOT-Disorder2, and metapredict V2 allowed us to evaluate the potential functional disorder of PRAME. Additionally, we used the Search Tool for the Retrieval of Interacting Genes (STRING) to analyze PRAME's potential interactions with other proteins.

RESULTS

Our structural analysis showed that PRAME contains intrinsically disordered protein regions (IDPRs), which are structureless and flexible. We found that PRAME is significantly enriched with serine (p-value < 0.05), a disorder-promoting amino acid. PRAME was found to have an average disorder score of 16.49% (i.e., moderately disordered) across six per-residue intrinsic disorder predictors. Our IUPred analysis revealed the presence of disorder-to-order transition (DOT) regions in PRAME near the C-terminus of the protein (residues 475-509). The D2P2 platform predicted a region from approximately 140 and 175 to be highly concentrated with post-translational modifications (PTMs). FuzDrop predicted the PTM hot spot of PRAME to be a droplet-promoting region and an aggregation hotspot. Finally, our analysis using the STRING tool revealed that PRAME has significantly more interactions with other proteins than expected for randomly selected proteins of the same size, with the ability to interact with 84 different partners (STRING analysis result: p-value < 1.0 × 10-16; model confidence: 0.400).

CONCLUSION

Our study revealed that PRAME has IDPRs that are possibly linked to its functionality in the context of Class 1 UM. The regions of functionality (i.e., DOT regions, PTM sites, droplet-promoting regions, and aggregation hotspots) are localized to regions of high levels of disorder. PRAME has a complex protein-protein interaction (PPI) network that may be secondary to the structureless features of the polypeptide. Our findings contribute to our understanding of UM and suggest that IDPRs and DOT regions in PRAME may be targeted in developing new therapies for this aggressive cancer. Video Abstract.

Intrinsic Disorder in the Human Tear Proteome

Purpose

We aimed to characterize the proteome of human tears and assess for the presence of intrinsically disordered proteins (IDPs). IDPs, despite lacking a rigid three-dimensional structure, maintain biological functionality and could shed light on the molecular interactions within tears.

Methods

We analyzed a dataset of 1475 proteins identified in the tear film of three healthy subjects. We employed several computational tools, including the Compositional Profiler, Rapid Intrinsic Disorder Analysis Online, Search Tool for the Retrieval of Interacting Genes, and Database of Disordered Protein Predictors to evaluate the intrinsic disorder, protein interactions, and functional characterization of the disordered regions within this proteome.

Results

Our analysis showed a notable inclination toward intrinsic disorder. Two out of 10 order-promoting residues and five out of 10 disorder-promoting residues were found enriched. Using the Predictor of Natural Disordered Regions (PONDR) VSL2 output, 95% of these proteins were classified as highly or moderately disordered. We revealed an extensive protein-protein interaction network with significant interaction enrichment. The most disordered proteins exhibited higher disorder binding sites and diverse posttranslational modifications compared to the most ordered ones.

Conclusions

To the best of our knowledge, our study is the first comprehensive analysis of intrinsic disorder in the human tear film proteome, and it revealed an abundance of IDPs and their role in protein function and interaction networks. These findings suggest that variations in the intrinsic disorder of a tear film could be impacted by systemic and ocular conditions, offering promising avenues for disease biomarker identification and drug target development. Further research is needed to understand the implications of these findings in human health and disease.

Correlation Between Altmetric Attention Scores and Citations for Articles Published in High-Impact Factor Ophthalmology Journals From 2018 to 2019

Importance

The Altmetric attention score (AAS) provides new information to gauge the impact of a research article not found through typical metrics, such as impact factor or citation counts.

Objective

To explore the association between AAS and common impact markers among high-impact ophthalmology journals from 2018 to 2019.

Design, Setting, and Participants

All articles published in the American Journal of Ophthalmology (AJO), JAMA Ophthalmology (JAMAO), and Ophthalmology (OPH) from January 1, 2018, to December 31, 2019, were collected for this cross-sectional study. Excluded articles were those missing Altmetric data at the time of data collection. The AAS and associated social media impact for each article were collected with the AAS calculator bookmarklet. Spearman rank correlation analyses and analysis of variance tests were conducted to assess differences in various metrics between AJO, JAMAO, and OPH. The study included articles published of all document types (article, conference paper, editorial, erratum, letter, note, retracted, review, and short survey) and access status (open access and not open access).

Main Outcomes and Measures

The correlation between citation counts and Altmetric variables including AAS.

Results

A total of 2467 articles were published in the study period. There were 351 articles excluded owing to missing Altmetric data. Of the 2116 articles included in the analysis, 1039 (49.1%) were published in 2018, and 1077 (50.9%) were published in 2019; the mean number of citations was 8.8 (95% CI, 7.9-9.6) for AJO, 6.2 (95% CI, 5.3-7.1) for JAMAO, and 15.1 (95% CI, 13.3-17.0) for OPH. The mean AAS was 4.5 (95% CI, 3.3-5.6) for AJO (723 publications), 27.4 (95% CI, 22.1-32.8) for JAMAO (758 publications), and 15.1 (95% CI, 10.9-19.3) for OPH (635 publications). Citation rate was moderately correlated with AAS across the 3 journals (AJO, ρ = 0.39; P < .001; JAMAO, ρ = 0.41; P < .001; OPH, ρ = 0.40; P < .001), as well as minimally or moderately correlated with engagement or mention by Facebook posts (AJO, ρ = 0.38; P < .001; JAMAO, ρ = 0.24; P < .001; OPH, ρ = 0.20; P < .001), news outlet reporting (AJO, ρ = 0.12; P < .001; JAMAO, ρ = 0.38; P < .001; OPH, ρ = 0.19; P < .001), and Twitter posts (AJO, ρ = 0.40; P < .001; JAMAO, ρ = 0.38; P < .001; OPH, ρ = 0.42; P < .001).

Conclusions and Relevance

Results of this cross-sectional study suggest that citation rate has a moderate positive correlation with online and social media sharing of research in ophthalmology literature. Peer-reviewed journals may increase their reach and impact by sharing their literature through social media and online platforms.

The aqueous humor proteome is intrinsically disordered

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Our study demonstrated that intrinsic disorder is abundant in the aqueous humor.

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The 749 aqueous proteins analyzed were enriched with disorder-promoting residues.

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208 aqueous humor proteins were predicted to be highly intrinsically disordered.

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Misregulation of IDPs may promote pathology in the aqueous humor.

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IDPs in aqueous humor may serve as future targets for novel therapeutics.