Kim Colin K, Djulbegovic Mak B, Broytman David, Hadzijahic Nedym, Antonietti Michael, Gonzalez David J Taylor, Uversky Vladimir N, Yannuzzi Nicolas A, Karp Carol L
Bascom Palmer Eye Institute, University of Miami, Miami, Florida, USA.
Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
Proteomics Clin Appl. 2025 Jul;19(4):e70012. doi: 10.1002/prca.70012. Epub 2025 Jun 7.
The human retina relies on a complex network of proteins, many of which exhibit intrinsic disorder and liquid-liquid phase separation (LLPS), enabling dynamic interactions for retinal function. Disruptions in these properties, along with missense mutations, have been linked to retinal diseases. This study aims to characterize and compare retinal proteins categorized by their expression specificity and tissue distribution using bioinformatics tools to explore relationships between intrinsic protein disorder, phase separation potential, and mutation pathogenicity.
We analyzed retinal proteins classified by the Human Protein Atlas (HPA) into two major groups based on gene expression specificity (degree of unique retinal expression) and gene expression distribution (extent of expression across tissues). We analyzed nine retinal proteomes categorized by gene expression specificity and distribution. Intrinsic protein disorder was assessed using per-residue and global disorder predictors from the Rapid Intrinsic Disorder Analysis Online (RIDAO) platform, LLPS potential was evaluated with ParSe v2, and missense mutation pathogenicity was predicted using AlphaMissense.
Significant differences in per-residue intrinsic protein disorder were found within the specificity and distribution subgroups (p < 0.0001). In addition, global disorder predictions from the RIDAO platform demonstrated non-random distributions of protein species across the proteomes analyzed in both subgroups (p < 0.0001). Furthermore, proteins specifically elevated in the retina exhibited higher intrinsic disorder and greater phase separation propensity (ParSe v2, AUC up to 0.650), compared to those more broadly expressed. Lastly, AlphaMissense analysis showed significant variations in the average pathogenicity scores of missense mutations within subgroups (p < 0.0001).
Our results show that intrinsic disorder, LLPS, and mutational tendencies are not evenly distributed among retinal proteomes. Our study demonstrates a link between intrinsic disorder, LLPS potential, and pathogenic vulnerability among retinal proteins, underscoring the unique structural and functional landscape of retinal proteomes. Proteins with higher specificity to the retina exhibit greater disorder and phase separation potential, highlighting their potential role in dynamic cellular processes that support retinal function. Conversely, proteins widely distributed across multiple tissues tend to be more ordered, suggesting a need for structural stability in their broader functional roles.
人类视网膜依赖于一个复杂的蛋白质网络，其中许多蛋白质表现出内在无序性和液-液相分离（LLPS），从而实现视网膜功能所需的动态相互作用。这些特性的破坏以及错义突变与视网膜疾病有关。本研究旨在利用生物信息学工具对按表达特异性和组织分布分类的视网膜蛋白质进行表征和比较，以探索蛋白质内在无序性、相分离潜力和突变致病性之间的关系。
我们分析了人类蛋白质图谱（HPA）根据基因表达特异性（独特视网膜表达程度）和基因表达分布（跨组织表达范围）分为两大类的视网膜蛋白质。我们分析了按基因表达特异性和分布分类的九个视网膜蛋白质组。使用在线快速内在无序分析（RIDAO）平台的逐个残基和全局无序预测器评估蛋白质内在无序性，用ParSe v2评估LLPS潜力，并用AlphaMissense预测错义突变致病性。
在特异性和分布亚组中发现逐个残基的蛋白质内在无序性存在显著差异（p < 0.0001）。此外，RIDAO平台的全局无序预测表明，在两个亚组分析的蛋白质组中，蛋白质种类呈非随机分布（p < 0.0001）。此外，与那些广泛表达的蛋白质相比，在视网膜中特异性升高的蛋白质表现出更高的内在无序性和更大的相分离倾向（ParSe v2，AUC高达0.650）。最后，AlphaMissense分析显示亚组内错义突变的平均致病性评分存在显著差异（p < 0.0001）。
我们的结果表明，内在无序性、LLPS和突变倾向在视网膜蛋白质组中分布不均。我们的研究证明了视网膜蛋白质中内在无序性、LLPS潜力和致病易感性之间的联系，强调了视网膜蛋白质组独特的结构和功能格局。对视网膜具有更高特异性的蛋白质表现出更大的无序性和相分离潜力，突出了它们在支持视网膜功能的动态细胞过程中的潜在作用。相反，广泛分布于多种组织的蛋白质往往更有序，这表明它们在更广泛的功能作用中需要结构稳定性。
