Proteomic Analysis Uncovers Multiprotein Signatures Associated with Early Diabetic Kidney Disease in Youth with Type 2 Diabetes Mellitus

Abstract

Key Points:

1. Proteomics analyses identified seven proteins predictive of time to development of albuminuria among youth with type 2 diabetes in the Treatment Options for Type 2 Diabetes in Adolescents and Youth cohort, 118 proteins predictive of time to development of hyperfiltration, and three proteins predictive of time to rapid eGFR decline.

2. Seven proteins were predictive of all three outcomes (SEM4A, PSB3, dihydroxyphenylalanine decarboxylase, C1RL1, T132A, pyruvate carboxylase, and C1-esterase inhibitor) and have been implicated in immune regulatory mechanisms, metabolic dysregulation, proteostasis, and cellular signaling pathways.

3. Elastic net Cox proportional hazards model identified distinct multiprotein signatures (38–68 proteins) of time to albuminuria, hyperfiltration, and rapid eGFR decline with concordance for models with clinical covariates and selected proteins between 0.81 and 0.96, whereas the concordance for models with clinical covariates only was between 0.56 and 0.63.

Background: The onset of diabetic kidney disease (DKD) in youth with type 2 diabetes (T2D) mellitus often occurs early, leading to complications in young adulthood. Risk biomarkers associated with the early onset of DKD are urgently needed in youth with T2D.

Methods: We conducted an in-depth analysis of 6596 proteins (SomaScan 7K) in 374 baseline plasma samples from the Treatment Options for Type 2 Diabetes in Adolescents and Youth study to identify multiprotein signatures associated with the onset of albuminuria (urine albumin-to-creatinine ratio ≥30 mg/g), a rapid decline in eGFR (annual eGFR decline >3 ml/min per 1.73 m² and/or ≥3.3% at two consecutive visits), and hyperfiltration (≥135 ml/min per 1.73 m² at two consecutive visits). Elastic net Cox regression with ten-fold cross-validation was applied to the top 100 proteins (ranked by P value) to identify multiprotein signatures of time to development of DKD outcomes.

Results: Participants in the Treatment Options for Type 2 Diabetes in Adolescents and Youth study (14±2 years, 63% female, 7±6 months diabetes duration) experienced high rates of early DKD: 43% developed albuminuria, 48% hyperfiltration, and 16% rapid eGFR decline. Increased levels of seven and three proteins were predictive of shorter time to develop albuminuria and rapid eGFR decline, respectively; 118 proteins predicted time to development of hyperfiltration. Elastic net Cox proportional hazards models identified multiprotein signatures of time to incident early DKD with concordance for models with clinical covariates and selected proteins between 0.81 and 0.96, whereas the concordance for models with clinical covariates only was between 0.56 and 0.63.

Conclusions: Our research sheds new light on proteomic changes early in the course of youth-onset T2D that associate with DKD. Proteomic analyses identified promising risk factors that predict DKD risk in youth with T2D and could deepen our understanding of DKD mechanisms and potential interventions.

Clinical Trial registry name and registration number:: NCT00081328.

Graphical abstract

Figure 1

Study design and participants included in analyses. TODAY, Treatment Options for Type 2 Diabetes in Adolescents and Youth.

Figure 2

Volcano plots summarizing the association of proteins with outcomes in TODAY, using adjusted Cox proportional hazards models. Each point represents a protein. The x axis is the HR of the association per SD of the protein, and the y axis is the negative of the base 10 log-transformed P value, such that proteins with larger effect size are further to the right and left on the x axis and proteins with more significant association are higher on the y axis. Unadjusted P values < 0.05 are shown in blue, and the horizontal dashed line represents P = 0.05. CLU, clusterin; HR, hazard ratio; IGFBP-6, IGF-binding protein 6; MYOC, myocilin; NELL1, neural epidermal growth factor-like 1; PEDF, pigment epithelium-derived factor; RELM-beta, resistin-like molecule beta.

Figure 3

Venn diagram showing the degree of overlap between proteins with nominally significant (P < 0.05) associations with time to albuminuria, hyperfiltration, and rapid eGFR decline.

Figure 4

Concordance of multivariable Cox proportional hazards models for DKD outcomes. Models compared are (1) covariates only (HbA1c, log-transformed triglycerides, systolic BP, and estimated insulin sensitivity), (2) proteins only, with proteins selected by elastic net regression, and (3) proteins and covariates. CI, confidence interval; DKD, diabetic kidney disease; HbA1c, hemoglobin A1c.