Clinical proteomics最新文献

Background: There is insufficient attention to the pathogenesis of abnormal radiological changes and molecular mechanism in the paraspinal muscles in AIS patients.

Methods: Proteomics of plasma exosomes were applied for identification of differentially expressed proteins (DEPs) in AIS patients through liquid chromatography mass spectrometry (LC-MS/MS). Bioinformatic analysis were performed to explore biomarkers. The muscle density (HU value) of the concave and convex sides of paravertebral muscles in AIS patients was compared. HE staining were applied for investigation of pathological changes of paravertebral muscles. Cartilage intermediate layer protein-1 (CILP-1), TGF-β1/Smad pathway and the downstream proteins were compared between the concave and convex side of paraspinal muscle. C2C12 cells were incubated with TGF-β1 or Smad3 phosphorylation inhibitor (SIS3) to further clarify the correlation between CILP-1 and TGF-β1/Smad pathway.

Results: A total of 2437 proteins were identified, among which DEPs were enriched in immune response and extracellular matrix-receptor interaction, while CILP-1 was screened out. HU value of concave multifidus muscle (MF) in apical vertebrae area was significantly lower when compared with both convex MF and control group. Muscle fibrosis, increased CILP-1, TGF-β1 phosphorylation of Smad2/3 and downstream proteins could be observed in the concave side of paraspinal muscle. TGF-β1 stimulation resulted in upregulation of CILP-1 and ECM related proteins, which could be partially inhibited by SIS3.

Discussion: We confirmed the asymmetric expressions of CILP-1 and TGF-β1/Smad signaling pathways in the paravertebral muscles of AIS patients. In C2C12 cells, TGF-β1 induced up-regulation of CILP-1 expression via Smad3 phosphorylation.

Background: Microsamples are simple blood sampling procedures utilizing small blood draws. Although microsamples are regularly used in some disciplines, proteomic analysis of these samples is an emerging field. Currently, it is unclear whether the quantitative precision and proteome coverage achieved in microsamples is comparable to plasma or serum. As a consequence, microsamples are not used in proteomics to the same degree as more traditional blood samples.

Objectives: The objective of this scoping review was to report the applications of microsamples within clinical mass spectrometry-based proteomics. This was accomplished by describing both proof-of-concept and clinical proteomics research within this field, with an additional evaluation of the newest advances regarding clinical proteomics.

Inclusion criteria: Original scientific literature was included where bottom-up mass spectrometry was used to analyze endogenous proteins from human microsamples.

Methods: Relevant publications were sourced through three scientific databases (MEDLINE, EMBASE and Scopus) in addition to backward and forward citation searches through Scopus. Record screening was performed independently by two separate authors. The review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines.

Results: A total of 209 records were screened for inclusion from database searches and 3157 records were screened from forward and backward citation searches, resulting in 64 eligible studies. An evaluation of proof-of-concept research within this field revealed that although microsamples are amenable to high-throughput proteomics using a variety of targeted and untargeted acquisition methods, quantification remained a relevant issue. Microsampling practices were heterogeneous, and no standard procedure existed for protein quantification. Clinical studies investigated protein expression in numerous disease or experimental groups, including hemoglobinopathies and immunodeficiency disorders.

Conclusion: The use of microsamples is increasing within the proteomics field and these samples are amenable to standard bottom-up workflows. Although microsamples present a clear advantage in terms of sampling procedure, both the sample collection and quantification procedures remain to be standardized. However, there is an incentive to address the remaining issues, since microsampling would greatly reduce the resources necessary to sample large cohorts within clinical proteomics, a field that currently lacks large discovery and validation cohorts.

Background and aims: In recent years, the prevalence of non-alcoholic fatty liver disease (NAFLD) has risen among patients with chronic hepatitis B (CHB), coinciding with the increasing rates of obesity and metabolic syndrome. Both conditions can contribute to liver fibrosis and even hepatocellular carcinoma; however, the pathogenesis of each disease, as well as CHB concurrent with NAFLD, remains incompletely understood.

Methods: We comprehensively analyzed protein levels in liver tissues from four distinct groups: healthy controls, patients with CHB, patients with NAFLD, and those with CHB and NAFLD using proteomic profiling. Subsequently, we performed bioinformatics analyses based on the results of differentially expressed proteins (DEPs). We also verified the levels of select DEPs in both patient liver samples and a murine model.

Results: Our investigation revealed that enhanced viral clearance in patients with hepatitis B virus (HBV) with concurrent NAFLD might be associated with an inflammatory response and the activation of numerous metabolic pathways within the body. Meanwhile, the degree of hepatic steatosis was associated with anomalies in fatty acid degradation, glycolysis/gluconeogenesis, and other metabolic processes. However, the prognosis for patients with CHB and concurrent NAFLD may be severe, and this may be connected to the altered levels of proteins such as ACAT1, ACY1, SERPINB3, MTCH2, ALDH2, ECHS1, S100A7, and LRP6.

Conclusion: In comparison to CHB and NAFLD alone, the prognosis for CHB complicated by NAFLD appears less favorable. This disparity is closely correlated with distinct protein level patterns in the liver following the onset of both diseases. Our study provides novel insights into the disease progression and clinical mechanisms underlying CHB and NAFLD.

Background: Circulating proteins are routinely quantified from liquid biopsies to deduce health and disease. Among these are endocrine protein hormones, which regulate human growth, development, metabolism, and reproduction. Most commonly, these proteins are analyzed in plasma or serum prepared from venous blood draws. Recently, devices for quantitative capillary sampling from a finger prick have emerged, but their utility for clinical testing remains to be explored.

Methods: To study the analytical capabilities of quantitative dried blood spots (qDBS), we quantified the luteinizing hormone subunit beta (LHB), follicle-stimulating hormone subunit beta (FSHB), thyroid-stimulating hormone subunit beta (TSHB), prolactin (PRL), and growth hormone 1 (GH1) by multiplexed immunoassays. We determined the performance of the endocrine hormone assays in paired qDBS and EDTA plasma samples from 100 donors (90% females) aged 4 to 78. Lastly, we compared the protein levels with those from an accredited clinical chemistry laboratory.

Results: The multiplexed analysis showed precise protein quantifications in qDBS (mean CV = 8.3%), high concordance with plasma levels (r = 0.88 to 0.99), and accuracy being matrix- and protein-dependent (recovery: 80-225%). Using the current protocol and sample dilutions, reported protein concentrations were 1.2 to 7.5 times higher in plasma than in qDBS eluates. Concentrations from multiplexed plasma assays agreed with the clinical data (r = 0.87 to 0.99) and decreased slightly when comparing clinical plasma data with multiplexed qDBS assays (r = 0.76 to 0.98). Significant increases in age-related FSHB and LHB levels were observed in females in all specimens and assays (p < 0.01).

Conclusions: This study shows the suitability of modern qDBS devices for quantifying clinically informative proteins in multiplexed assays and highlights the need for future work on specimen-specific optimization and standards. Volumetric DBS sampling offers new routines for accurate protein quantification for precision medicine.

Background: Hypertensive nephrosclerosis (HN) is a major cause of end-stage renal disease; however, few longitudinal studies have employed serum proteomics to document its progression. This study aimed to identify potential circulating biomarkers indicative of disease progression in HN by performing serum proteomic analysis at two time points in patients with progressive and stable disease.

Methods: Forty-one patients diagnosed with HN were recruited from the UK Salford Kidney Study, with serum samples collected at baseline and follow-up (1.5-10 years after baseline). Twenty-five patients experienced stable disease course, while 16 patients experienced progressive disease. Proteomics was performed via tandem mass tag labelling and liquid chromatography-tandem mass-spectrometry (LC-MS). Pathway analysis was performed on all significantly abundant proteins, as was network analysis of circulating proteins that are abundant in the kidney according to the Human Protein Atlas.

Results: Pathway analysis revealed significant enrichment in pathways related to inflammation and infection, including complement and coagulation cascades, as well as metabolic processes in patients with disease progression. Marker abundance levels related to adhesion and the ECM were also altered in progresssive disease follow-up, compared to stable disease follow-up.

Conclusion: The observed changes in inflammatory and adhesion-related pathways may offer valuable insights into the mechanisms driving HN progression and potential targets for intervention.

Assembly modulators are a new class of allosteric site-targeted therapeutic small molecules, some of which are effective at restoring nuclear localization of TDP-43 in ALS cellular models, and which display efficacy in a variety of ALS animal models. These compounds have been shown to bind selectively to a small subset of protein disulfide isomerase (PDI), a protein implicated in ALS pathophysiology. The targeted subset of PDI is found within a novel, transient and energy-dependent multi-protein complex that includes other important members of the ALS interactome, such as TDP-43, RanGTPase, and selective autophagy receptor p62/SQSTM1. We demonstrate here that a similar multi-protein complex drug target is present in PBMCs as isolated by energy-dependent drug resin affinity chromatography (eDRAC) and characterized by mass spectrometry and by Western blot (WB). Signature alterations in the composition of the multi-protein complex in PBMCs from ALS patients compared to PBMCs from healthy individuals were identified by WB of eDRAC bound proteins, thereby extending earlier literature suggesting PBMC dysfunction in ALS. Changes in the PBMC drug target in ALS patients compared to healthy individuals include diminished p62/SQSTM1 and appearance of a 17 kDa post-translationally modified form of RanGTPase. These changes are not readily apparent from analysis of whole cell extracts, as the individual protein components within the drug target multi-protein complex comprise only small percentages of the total of those component proteins in the extract. Furthermore, whole blood from ALS patients shows a distinctive degradation of total RanGTPase not observed in blood from healthy individuals. This degradation appears to be rescued by treatment of whole blood from ALS patients for 72 h with ALS-active assembly modulator small molecules. Our findings are consistent with the hypothesis that ALS is fundamentally a disorder of homeostasis that can be detected early, prior to disability, in blood by the methods described, and restored to the healthy state by assembly modulator drug treatment.

Endometrial cancer (EC), a prevalent and intricate disease, is associated with a poor prognosis among gynecological malignancies. Its incidence rising globally underscores the urgent need for biomarkers detection in both research and clinical settings. Over the past decade, we've witnessed rapid advancements in biological methodologies and techniques. A multitude of omics technologies, encompassing genomic/transcriptomic sequencing and proteomic/metabolomic mass spectrometry, have been extensively employed to analyze both tissue and liquid samples derived from EC patients. The integration of multi-omics data has not only broadened our understanding of the disease but also unearthed valuable biomarkers specific to EC. This review encapsulates the recent progress and future prospects in the application of multi-omics technologies in EC research, emphasizing the potential of multi-omics in uncovering novel biomarkers and enhancing clinical assessments.

Background: Prostate cancer is one of the most frequently diagnosed cancers in men. Prostate tumor staging and disease aggressiveness are evaluated based on the Gleason scoring system, which is further used to direct clinical intervention. The Gleason scoring system provides an estimate of tumor aggressiveness through quantitation of the serum level of prostate specific antigen (PSA) and histologic assessment of Grade Group, determined by the Gleason Grade of the tumor specimen.

Methods: To improve our understanding of the proteomic characteristics differentiating low- versus high-grade prostate cancer tumors, we performed a deep proteomic characterization of laser microdissected epithelial and stromal subpopulations from surgically resected tissue specimens from patients with Gleason 6 (n = 23 specimens from n = 15 patients) and Gleason 9 (n = 15 specimens from n = 15 patients) prostate cancer via quantitative high-resolution liquid chromatography-tandem mass spectrometry analysis.

Results: In total, 789 and 295 grade-specific significantly altered proteins were quantified in the tumor epithelium and tumor-involved stroma, respectively. Benign epithelial and stromal populations were not inherently different between Gleason 6 versus Gleason 9 specimens. Notably, 598 proteins were exclusively significantly altered between Gleason 9 (but not Gleason 6) tumor-involved stroma and benign stroma, including several proteins involved in cholesterol biosynthesis and nucleotide metabolism.

Conclusions: Proteomic alterations between Gleason 6 versus Gleason 9 were exclusive to the disease microenvironment, observed in both the tumor epithelium and tumor-involved stroma. Further, the molecular alterations measured in the tumor-involved stroma from Gleason 9 cases relative to the benign stroma have unique significance in disease aggressiveness, development, and/or progression. Our data provide supportive evidence of a need for further investigations into targeting stromal reservoirs of cholesterol and/or deoxynucleoside triphosphates in PCa tumors and further highlight the necessity for independent examination of the TME epithelial and stromal compartments.