Proteomic approaches to identify blood-based biomarkers for depression and bipolar disorders.

INTRODUCTION: Major depressive disorder (MDD) and bipolar disorder (BD) are leading causes of disability worldwide, yet many people remain undiagnosed, are misdiagnosed, and/or ineffectively treated. Diagnosis relies on the clinical assessment of symptoms, and there is currently no molecular or brain-imaging diagnostic test available. Identifying and validating protein biomarkers could provide a more accurate and objective means of diagnosis. Areas covered: Proteomics is a powerful tool that enables the identification and quantification of novel candidate biomarkers of disease. In this review, we discuss the role of proteomic technologies in biomarker discovery and validation, peripheral blood as a source of protein biomarkers, statistical methods for analyzing proteomic data, and some existing challenges in the field. We also review a selection of previously published studies focused on identifying blood-based diagnostic protein biomarkers of MDD and BD within a ten-year period. Expert commentary: Proteomic studies have led to the identification of numerous potential biomarkers of MDD and BD. However, clinical validation and translation into clinical practice have not yet been achieved. Conducting large-scale validation studies and addressing various factors that limit the reproducibility of the proteomic findings are key to ensure that robust and reliable biomarker tests are developed and clinically validated.

Proteomic Discovery and Development of a Multiplexed Targeted MRM-LC-MS/MS Assay for Urine Biomarkers of Extracellular Matrix Disruption in Mucopolysaccharidoses I, II, and VI.

The mucopolysaccharidoses (MPS) are lysosomal storage disorders that result from defects in the catabolism of glycosaminoglycans. Impaired muscle, bone, and connective tissue are typical clinical features of MPS due to disruption of the extracellular matrix. Markers of MPS disease pathology are needed to determine disease severity and monitor effects of existing and emerging new treatments on disease mechanisms. Urine samples from a small cohort of MPS-I, -II, and -VI patients (n = 12) were analyzed using label-free quantative proteomics. Fifty-three proteins including many associated with extracellular matrix organization were differently expressed. A targeted multiplexed peptide MRM LC-MS/MS assay was used on a larger validation cohort of patient samples (MPS-I n = 18, MPS-II n = 12, MPS-VI n = 6, control n = 20). MPS-I and -II groups were further subdivided according to disease severity. None of the markers assessed were altered significantly in the mild disease groups compared to controls. ß-galactosidase, a lysosomal protein, was elevated 3.6-5.7-fold significantly (p < 0.05) in all disease groups apart from mild MPS-I and -II. Collagen type Iα, fatty-acid-binding-protein 5, nidogen-1, cartilage oligomeric matrix protein, and insulin-like growth factor binding protein 7 concentrations were elevated in severe MPS I and II groups. Cartilage oligomeric matrix protein, insulin-like growth factor binding protein 7, and ß-galactosidase were able to distinguish the severe neurological form of MPS-II from the milder non-neurological form. Protein Heg1 was significantly raised only in MPS-VI. This work describes the discovery of new biomarkers of MPS that represent disease pathology and allows the stratification of MPS-II patients according to disease severity.

Proteomic profiling reveals sub proteomes of the human placenta.

Proteomic characterisation of the placenta has largely been focused on effect of disease, anatomical features or specific cell types. We describe an unbiased proteomic mapping analysis to investigate how the placental proteome changes throughout the organ. A transverse slice of a human placenta was sectioned into 1 × 1cm samples. Sections were analysed using label free proteomics. Analysis revealed two distinct sub-proteomes that did not have anatomical significance. One had a muscular proteome and the other had distinct immunomodulation functions. Chorionic plate enriched proteins highlighted the fetal tissues high energy requirements whilst mechanisms of the decidua observed included modulation of cortisone levels.

A rapid high throughput proteomic method based on profiling of proteolytic free peptides to assess post-delivery degradation of placental tissue.

A rapid method to determine quality for placental proteomic studies is required due to varying lengths of time between delivery and sampling in routine protocols. We developed a rapid 10 min LC-MS based scanning method to profile free peptides liberated from natural proteolytic degradation. The assay was applied to placenta samples obtained following refrigeration for varying time periods post-delivery (12 h, +24 h, +48 h and +72 h). Analysis reveals time dependant overlapping profiles for groups <24 to +48 h with greatest variation in the +72 h group, indicating that significant proteolysis affects tissue integrity between 48 and 72 h.