Potential of UCHL1 as biomarker for destruction of pancreatic beta cells

Construction and evaluation of a metabolic correlation diagnostic model for diabetes based on machine learning algorithms

BACKGROUND

Diabetes mellitus (DM) is a prevalent chronic disease marked by significant metabolic dysfunctions. Understanding its molecular mechanisms is vital for early diagnosis and treatment strategies.

METHODS

We used datasets GSE7014, GSE25724, and GSE156248 from the GEO database to build a diagnostic model for DM using Random Forest (RF) and LASSO regression models. GSE20966 served as a validation cohort. DM patients were classified into two subtypes for functional enrichment analysis. Expression levels of key diagnostic genes were validated using quantitative real-time PCR (qRT-PCR) on Peripheral Blood Mononuclear Cells (PBMCs) from DM patients and healthy controls, focusing on CXCL12 and PPP1R12B with GAPDH as the internal control.

RESULTS

After de-batching the datasets, we identified 131 differentially expressed genes (DEGs) between DM and control groups, with 70 up-regulated and 61 down-regulated. Enrichment analysis revealed significant down-regulation in the IL-12 signaling pathway, JAK signaling post-IL-12 stimulation, and the ferroptosis pathway in DM. Five genes (CXCL12, MXRA5, UCHL1, PPP1R12B, and C7) were identified as having diagnostic value. The diagnostic model showed high accuracy in both the training and validation cohorts. The gene set also enabled the subclassification of DM patients into groups with distinct functional traits. qRT-PCR results confirmed the bioinformatics findings, particularly the up-regulation of CXCL12 and PPP1R12B in DM patients.

CONCLUSION

Our study pinpointed seven energy metabolism-related genes differentially expressed in DM and controls, with five holding diagnostic value. Our model accurately diagnosed DM and facilitated patient subclassification, offering new insights into DM pathogenesis.

Plasma UCHL-1 as a Biomarker of Brain Injury in Hospitalized Foals With Neonatal Encephalopathy

A plasma biomarker such as ubiquitin carboxyl-terminal hydrolase L1 (UCHL-1) to distinguish neonatal encephalopathy (NE) from other disorders and provide prognostic information would be useful for equine practitioners. In this prospective study, plasma UCHL-1 was measured in 331 hospitalized foals ≤4 days of age. Clinical diagnoses of neonatal encephalopathy only (NE group, n = 77), sepsis only (Sepsis group, n = 34), concurrent sepsis and NE (NE+Sepsis group, n = 85), or neither sepsis nor NE (Other group, n = 101) were made by the attending veterinarian. Plasma UCHL-1 concentrations were measured by ELISA. Differences between clinical diagnoses groups were evaluated and receiver operator curve (ROC) analysis was performed to assess diagnostic and prognostic performance. Median admission UCHL-1 concentration was significantly higher for NE (18.22 ng/mL; 7.93-37.43) and NE+Sepsis (17.42 ng/mL; 7.67-36.24) groups than Other foals (7.77 ng/mL; 3.92-22.76). Admission UCHL-1 was significantly higher in nonsurvivors (16.66 ng/mL; 6.89-34.84) than survivors (10.27 ng/mL; 5.82-29.94). Overall diagnostic performance of admission UCHL-1 concentration for NE diagnosis was determined (AUC 0.61; 95% confidence interval [CI] = 0.55-0.68); sensitivity and specificity for predicting NE were 73% and 49% respectively. Overall prognostic performance of time to lowest UCHL-1 concentration for predicting nonsurvival was determined (AUC 0.72; 95% CI = 0.65-0.79); sensitivity and specificity were 86% and 43% respectively. In this foal population, differences in plasma UCHL-1 concentrations were observed between foals with NE or NE with sepsis, and other diagnoses. The diagnostic and prognostic value of admission UCHL-1 concentration was limited.

Crucial roles of UCH-L1 on insulin-producing cells and carbohydrate metabolism in Drosophila melanogaster model

Ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) is a highly expressed protein in β cells and has been implicated in β cells' viability and function, however, the role of UCH-L1 in β cells remains unclear. Herein, we examined the functions of UCH-L1 in β cells by utilizing the Drosophila melanogaster model. Our results showed that specific knockdown of dUCH (D.melanogaster homolog of UCH-L1) in Drosophila Insulin-producing cells (D.melanogaster homolog of β cells) induced mitochondria fusion, IPCs death/degeneration, interfered with DILP2 secretion, and triggered the rise of glycogen storage and body weight. Strikingly, the impairment in IPCs cellular activities can be rescued by vitamin C- a strong antioxidant compound, which suggested the relationship between knockdown dUCH and oxidative stress in IPCs; and the potential of this model in screening compounds for β cells function moderation. Since carbohydrate metabolism is an important function of beta cells, we continued to examine the ability to regulate carbohydrate metabolism of knockdown dUCH flies. Our results showed that knockdown dUCH caused the decline of IPCs number under a high-sucrose diet, which finally led to metabolic and physiological disturbances, including total lipid rise, glycogen storage reduction, circulating carbohydrate increase, and weight loss. These symptoms could be early indications of metabolic disorders, particularly β cell dysfunction-related diseases. Taken together, our results indicate that dUCH is essential in the viability and functions of IPCs through the regulation of carbohydrate metabolism in the Drosophila model.

Mass spectrometry-based direct detection of multiple types of protein thiol modifications in pancreatic beta cells under endoplasmic reticulum stress

Thiol-based post-translational modifications (PTMs) play a key role in redox-dependent regulation and signaling. Functional cysteine (Cys) sites serve as redox switches, regulated through multiple types of PTMs. Herein, we aim to characterize the complexity of thiol PTMs at the proteome level through the establishment of a direct detection workflow. The LC-MS/MS based workflow allows for simultaneous quantification of protein abundances and multiple types of thiol PTMs. To demonstrate its utility, the workflow was applied to mouse pancreatic β-cells (β-TC-6) treated with thapsigargin to induce endoplasmic reticulum (ER) stress. This resulted in the quantification of >9000 proteins and multiple types of thiol PTMs, including intra-peptide disulfide (S–S), S-glutathionylation (SSG), S-sulfinylation (SO₂H), S-sulfonylation (SO₃H), S-persulfidation (SSH), and S-trisulfidation (SSSH). Proteins with significant changes in abundance were observed to be involved in canonical pathways such as autophagy, unfolded protein response, protein ubiquitination pathway, and EIF2 signaling. Moreover, ~500 Cys sites were observed with one or multiple types of PTMs with SSH and S–S as the predominant types of modifications. In many cases, significant changes in the levels of different PTMs were observed on various enzymes and their active sites, while their protein abundance exhibited little change. These results provide evidence of independent translational and post-translational regulation of enzyme activity. The observed complexity of thiol modifications on the same Cys residues illustrates the challenge in the characterization and interpretation of protein thiol modifications and their functional regulation.

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Simultaneous quantification of protein abundances and multiple types of thiol PTMs.

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Multiple types PTMs observed on the same Cys sites for redox-regulated proteins.

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Data revealed complexity of thiol PTMs and their regulation.

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Distinctive translational and post-translational regulation under ER stress in β-cells.

Isolation and Proteomics of the Insulin Secretory Granule

Insulin, a vital hormone for glucose homeostasis is produced by pancreatic beta-cells and when secreted, stimulates the uptake and storage of glucose from the blood. In the pancreas, insulin is stored in vesicles termed insulin secretory granules (ISGs). In Type 2 diabetes (T2D), defects in insulin action results in peripheral insulin resistance and beta-cell compensation, ultimately leading to dysfunctional ISG production and secretion. ISGs are functionally dynamic and many proteins present either on the membrane or in the lumen of the ISG may modulate and affect different stages of ISG trafficking and secretion. Previously, studies have identified few ISG proteins and more recently, proteomics analyses of purified ISGs have uncovered potential novel ISG proteins. This review summarizes the proteins identified in the current ISG proteomes from rat insulinoma INS-1 and INS-1E cell lines. Here, we also discuss techniques of ISG isolation and purification, its challenges and potential future directions.

Ubiquitin carboxy-terminal hydrolase L1 - physiology and pathology

Ubiquitin C-terminal hydrolase 1 (UCHL1) is an enzyme unique for its multiple activity - both ligase and hydrolase. UCHL1 was first identified as an abundant protein found in the brain and testes, however its expression is not limited to the neuronal compartment. UCHL1 is also highly expressed in carcinomas of various tissue origins, including those from brain, lung, breast, kidney, colon, prostate, pancreas and mesenchymal tissues. Loss-of-function studies and an inhibitor for UCHL1 confirmed the importance of UCHL1 for cancer therapy. So far biological significance of UCHL1 was described in the following processes: spermatogenesis, oncogenesis, angiogenesis, cell proliferation and differentiation in skeletal muscle, inflammation, tissue injury, neuronal injury and neurodegeneration.

Deubiquitinating enzymes as cancer biomarkers: new therapeutic opportunities?

Cancer remains a life-threatening disease and accounts for the major mortality rates worldwide. The practice of using biomarkers for early detection, staging, and customized therapy may increase cancer patients’ survival. Deubiquitinating enzymes (DUBs) are a family of proteases that remove ubiquitin tags from proteins of interest undergoing proteasomal degradation. DUBs play several functional roles other than deubiquitination. One of the important roles of DUBs is regulation of tumor progression. Several reports have suggested that the DUB family members were highly-elevated in various cancer cells and tissues in different stages of cancer. These findings suggest that the DUBs could be used as drug targets in cancer therapeutics. In this review, we recapitulate the role of the DUB family members, including ubiquitin-specific protease, otubain protease, and important candidates from other family members. Our aim was to better understand the connection between DUB expression profiles and cancers to allow researchers to design inhibitors or gene therapies to improve diagnosis and prognosis of cancers.

Combined Analysis of GAD65, miR-375, and Unmethylated Insulin DNA Following Islet Transplantation in Patients With T1D

AIM

Several biomarkers have been proposed to detect pancreatic β cell destruction in vivo but so far have not been compared for sensitivity and significance.

METHODS

We used islet transplantation as a model to compare plasma concentrations of miR-375, 65-kDa subunit of glutamate decarboxylase (GAD65), and unmethylated insulin DNA, measured at subpicomolar sensitivity, and study their discharge kinetics, power for outcome prediction, and detection of graft loss during follow-up.

RESULTS

At 60 minutes after transplantation, GAD65 and miR-375 consistently showed near-equimolar and correlated increases proportional to the number of implanted β cells. GAD65 and miR-375 showed comparable power to predict poor graft outcome at 2 months, with areas under the curve of 0.833 and 0.771, respectively (P = 0.53). Using receiver operating characteristic analysis, we defined likelihood ratios (LRs) for rationally selected result intervals. In GADA-negative recipients (n = 28), GAD65 <4.5 pmol/L (LR = 0.15) and >12.2 pmol/L (LR = ∞) predicted good and poor outcomes, respectively. miR-375 could be used in all recipients irrespective of GAD65 autoantibody status (n = 46), with levels <1.4 pmol/L (LR = 0.14) or >7.6 pmol/L (LR = 9.53) as dual thresholds. The posttransplant surge of unmethylated insulin DNA was inconsistent and unrelated to outcome. Combined measurement of these three biomarkers was also tested as liquid biopsy for β cell death during 2-month follow-up; incidental surges of GAD65, miR-375, and (un)methylated insulin DNA, alone or combined, were confidently detected but could not be related to outcome.

CONCLUSIONS

GAD65 and miR-375 performed equally well in quantifying early graft destruction and predicting graft outcome, outperforming unmethylated insulin DNA.

Concentration of Proteasome in the Blood Plasma of Children with Acute Appendicitis, Before and After Surgery, and Its Correlation with CRP

OBJECTIVE

The determination of 20S proteasome concentration in the blood plasma of children with appendicitis and its correlation with CRP.

DESIGN AND SETTING

Thirty-one children with acute appendicitis, were randomly included into the study (age 5 years up to 17 years, mean age 11.5 + 1 years).

PARTICIPANTS

There were 17 girls and 14 boys. Eighteen healthy, age-matched subjects, admitted for planned surgeries served as controls. Exclusion criteria were: severe preexisting infections, immunological or cardiovascular diseases that required long-term medication, and complicated cases of appendicitis with perforation of appendix and/or peritonitis.

MAIN OUTCOME MEASURES

The 20S proteasome concentrations in the blood plasma of patients with acute appendicitis were highest before the surgery and were above the range of concentrations measured in controls, and the difference was statistically significant.

RESULTS

The 20S proteasome concentration measured 24 and 72 h after the operation, slowly decreased over time, and still did not reach the normal range, when compared with the concentration measured in controls (p < 0.05).

CONCLUSIONS

20S proteasome concentration may reflect the metabolic response to acute state inflammation, and the process of gradual ebbing of the inflammation. The method of operation-classic open appendectomy, or laparoscopic appendectomy, does not influence the general trend in 20S proteasome concentration.

Pediatric endocrine and metabolic diseases and proteomics

The principles of Predictive, Preventive and Personalized Medicine (PPPM) dictate the need to recognize individual susceptibility to disease in a timely fashion and to offer targeted preventive interventions and treatments. Proteomics is a state-of-the art technology- driven science aiming at expanding our understanding of the pathophysiologic mechanisms that underlie disease, but also at identifying accurate predictive, diagnostic and therapeutic biomarkers, that will eventually promote the implementation of PPPM. In this review, we summarize the wide spectrum of the applications of Mass Spectrometry-based proteomics in the various fields of Pediatric Endocrinology, including Inborn Errors of Metabolism, type 1 diabetes, Adrenal Disease, Metabolic Syndrome and Thyroid disease, ranging from neonatal screening to early recognition of specific at-risk populations for disease manifestations or complications in adult life and to monitoring of disease progression and response to treatment.

SIGNIFICANCE

Proteomics is a state-of-the art technology- driven science aiming at expanding our understanding of the pathophysiologic mechanisms that underlie disease, but also at identifying accurate predictive, diagnostic and therapeutic biomarkers that will eventually lead to successful, targeted, patient-centric, individualized approach of each patient, as dictated by the principles of Predictive, Preventive and Personalized Medicine. In this review, we summarize the wide spectrum of the applications of Mass Spectrometry-based proteomics in the various fields of Pediatric Endocrinology, including Inborn Errors of Metabolism, type 1 diabetes, Adrenal Disease, Metabolic Syndrome and Thyroid disease, ranging from neonatal screening, accurate diagnosis, early recognition of specific at-risk populations for the prevention of disease manifestation or future complications.

Single-cell transcriptomics of East-Asian pancreatic islets cells

Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on α- and β-cell gene expression in mice and subjects of predominantly European ancestry. We aimed to assess these findings in East-Asian islet-cells. 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. Differentially expressed transcripts between α- and β-cells were detected using ANOVA and in silico replications of mouse and human islet cell genes were performed. We identified 118 α, 105 β, 6 δ endocrine cells and 47 exocrine cells. Besides INS and GCG, 26 genes showed differential expression between α- and β-cells. 10 genes showed concordant expression as reported in rodents, while FAM46A was significantly discordant. Comparing our East-Asian data with data from primarily European subjects, we replicated several genes implicated in nuclear receptor activations, acute phase response pathway, glutaryl-CoA/tryptophan degradations and EIF2/AMPK/mTOR signaling. Additionally, we identified protein ubiquitination to be associated among East-Asian β-cells. We report on East-Asian α- and β-cell gene signatures and substantiate several genes/pathways. We identify expression signatures in East-Asian β-cells that perhaps reflects increased susceptibility to cell-death and warrants future validations to fully appreciate their role in East-Asian diabetes pathogenesis.

Overexpression of ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) in serum of children after thermal injury

PURPOSE

The study aims to determinate concentrations of ubiquitin C-terminal hydrolase 1 (UCHL1), which hydrolyzes amino acids from ubiquitin and cleave di-ubiquitins, in serum of children after thermal injury.

PATIENTS/METHODS

42 children scalded by hot water, managed at the Department of Pediatric Surgery, with burns in 4-20% TBSA were included into the study (age 9 months up to 14 years, mean age 2.5±1 years). Blood plasma UCHL1 concentration was assessed in 2-6h, 12-16h, 3d, 5d, and 7d after injury using surface plasmon resonance imaging biosensor. 18 healthy subjects admitted for planned surgeries served as controls.

RESULTS

The UCHL1 concentration in the blood plasma of patients with thermal injuries reached its peak 12-16h after thermal injury and slowly decreased over time, and still did not reach the normal range on the 7th day after thermal injury. Mean concentrations of UCHL1 after thermal injury were above the range measured in controls (0.12ng/ml): 2-6h after injury - 5.59ng/dl, 12-16h after injury - 9.16ng/dl, 3 days after injury - 6.94ng/dl, 5 days after 5.41ng/dl, 7 days after injury - 4.09ng/dl.

CONCLUSIONS

We observed sudden increase in the concentration of UCHL1 2-16h after thermal injury with the slow decrease in the UCHL1 concentration over the time. UCHL1 concentration was proportional to the severity of the burn. Further studies are needed to determine the mechanisms by which UCHL1 contributes to metabolic response following thermal injury.

What's in a Name? Classification of Diabetes Mellitus in Veterinary Medicine and Why It Matters

Diabetes Mellitus (DM) is a syndrome caused by various etiologies. The clinical manifestations of DM are not indicative of the cause of the disease, but might be indicative of the stage and severity of the disease process. Accurately diagnosing and classifying diabetic dogs and cats by the underlying disease process is essential for current and future studies on early detection, prevention, and treatment of underlying disease. Here, we review the current etiology-based classification of DM and definitions of DM types in human medicine and discuss key points on the pathogenesis of each DM type and prediabetes. We then review current evidence for application of this etiology-based classification scheme in dogs and cats. In dogs, we emphasize the lack of consistent evidence for autoimmune DM (Type 1) and the possible importance of other DM types such as DM associated with exocrine pancreatic disease. While most dogs are first examined because of DM in an insulin-dependent state, early and accurate diagnosis of the underlying disease process could change the long-term outcome and allow some degree of insulin independence. In cats, we review the appropriateness of using the umbrella term of Type 2 DM and differentiating it from DM secondary to other endocrine disease like hypersomatotropism. This differentiation could have crucial implications on treatment and prognosis. We also discuss the challenges in defining and diagnosing prediabetes in cats.

Quantitative proteomics of rat and human pancreatic beta cells

Data set description: This data set is composed by label-free alternate-scanning LC-MS/MS proteomics analysis human and Wistar rat pancreatic islet endocrine cells. The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat). From these mass spectrometry data, 'relative molar amount units' between cell types and across species were calculated. Biological relevance: These data provide a quantitative view on the unfractionated proteomes of human and rat beta and alpha cells. It is likely biased towards the proteins with higher molar abundance, relating to core functional pathways, but also includes several proteins with an islet-enriched expression. The quality of the cell preps is state-of-the-art, and the label-free quantitation is both precise and accurate, allowing detailed quantitative analysis.