Recent Advances of Proteomics Applied to Human Diseases

Abstract

G iven the intimate roles proteins play in health and disease, it is not surprising that during the past 20 years proteomics has been applied extensively to investigate human diseases to better understand disease mechanisms/pathways and to define new therapeutic targets as well as novel biomarkers for accurate diagnostics/prognostics. There is no doubt that advancements of disease proteomics will expand the frontiers of medicine to impact global health.This Special Issue of Journal of Proteome Research (JPR) features recent progress and advancements of proteomic studies of human diseases, focusing on pathogenesis, pathogenic mechanisms, diagnosis, prognosis, and treatment. It includes two reviews and 64 research articles (a total of 66 articles). The large number of articles published in a single Special Issue reflects the significance and broad interest of this area.It is especially encouraging to use the occasion of this Special Issue to reflect on how our field has evolved. Compared with disease proteomics articles previously published, this collection of studies shows obvious improvements in this field as follows. First, more advanced proteomic technologies, particularly sophisticated mass spectrometry for protein characterizations, profiling, quantitative analysis, and investigations of posttranslational modifications (PTMs), were used. Second, the study designs were more sophisticated and planned more carefully, for example, stringent validation to confirm screening data sets, sufficient sample size, and suitable control groups (i.e., inclusion of diseased controls in addition to the normal control). Third, functional significance of the identified proteins or targets was confirmed in most of these studies. Finally, feasibility for clinical applications was well demonstrated, for example, sensitivity/specificity of novel biomarkers for diagnostics/prognostics.In addition to the two reviews that update the current knowledge 1,2 and a technical development for clinical tissue preservation, 3 a wide variety of human diseases were investigated in this collection of proteome studies. These include diseases of central nervous system, 4−14 eye, 15,16

Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimer’s disease-related proteins

“…Advances in deep RNA sequencing and proteomic methods have provided unprecedented opportunities to characterize the molecular and cellular complexity of the CNS [ 5 , 8 , 9 , 25 , 32 , 38 , 39 ]. Microglia are the principal immune effectors in the CNS [ 1 ] that perform homeostatic functions under normal conditions but adopt diverse activated profiles as revealed by recent whole-cell and single-cell transcriptomic studies [ 5 , 6 , 8 , 25 ].…”

Proteomics in Psoriasis

“…The data obtained from proteomics frequently lead to a better understanding of biology, physiology, and pathogenic mechanisms of diseases [14]. Additionally, proteomics also leads to biomarker discovery for disease diagnostics and prognostics as well as novel therapeutic targets [14,15,16]. With the same ultimate goals as for other diseases, all of the previous and recent proteomics studies of psoriasis are summarized in Table 1 and discussed as follows.…”

Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry

“…label free quantification and SILAC) have provided successful examples (Bai et al, 2014; Bai et al, 2013; Kim et al, 2014; Thongboonkerd et al, 2014). For example, 10 protein samples can be analyzed together in one batch by the TMT 10-plex reagents.…”