Clinical proteomics最新文献

Colorectal cancer (CRC) has emerged as the second most prevalent cause of cancer-related mortality globally. Early identification of precancerous lesions prone to malignant transformation is pivotal in CRC prevention. Proteins, as microscopic reflections of cellular functional states, offer insights into pathological alterations within precancerous lesions through changes in their expression and function. Our review summarizes the protein research on colorectal adenomas under different sample conditions, including traditional adenomas, serrated lesions, LST, FAP and IBD. It highlights the changes in the expression patterns of key proteins and their potential mechanisms underlying the transition from precancerous to cancerous states. Additionally, it summarizes the research on post-translational modifications of characteristic protein families and associated signaling pathways, while discussing current techniques for studying protein expression and function in colorectal cancer, such as proteomics and artificial intelligence. However, current research limitations, such as small sample sizes, limited sample types, and insufficient in-depth mechanistic analysis, hinder comprehensive understanding. Future research should expand study cohorts, diversify sample types, and leverage machine learning and multi-omics approaches to develop predictive models. By doing so, a more comprehensive understanding of protein profiles during the progression from colorectal precancerous to cancerous lesions can be obtained, facilitating early CRC diagnosis and the development of targeted therapeutic interventions.

Background: Bacterial meningitis complicated by neurological complications (BMN) is a major cause of poor outcomes and mortality among children with bacterial meningitis. So far, the host-related mechanisms and diagnostic biomarkers of BMN and bacterial meningitis without neurological complications (BM) remain poorly understood and limited.

Methods: We implemented a two-stage cerebrospinal fluid (CSF) quantitative proteomics study involving three groups: children with BMN, BM, and diseases not involving the central nervous system(Ctrl). Initially, in the discovery cohort, data-independent acquisition (DIA) mass spectrometry was used for proteomic profiling on 242 CSF samples (77 BMN, 52 BM, and 113 Ctrl). Differentially expressed proteins (DEPs) were identified among the BMN/Ctrl, BM/Ctrl, and BMN/BM groups, followed by an analysis of their functional enrichment. Next, the parallel reaction monitoring (PRM) method was used to validate the essential DEPs identified during the DIA phase in a validation cohort of 196 subjects (94 BMN, 47 BM, and 55 Ctrl). Subsequently, the validated DEPs were further filtered to construct a PRM-based machine learning model that distinguishes between BMN and BM.

Results: A total of 1376 DEPs were identified in BM/Ctrl (757 upregulated, 619 downregulated), 1295 in BMN/Ctrl (745 upregulated, 550 downregulated), and 356 in BMN/BM(60 upregulated, 296 downregulated), respectively. The functional results indicate that the upregulated DEPs were primarily enriched in immunity, inflammation, complement, and phagocytosis in BMN/Ctrl and BM/Ctrl. Immunoglobulin production, phagocytosis, and the classical pathway of complement activation were further upregulated in BMN/BM. The downregulated DEPs are primarily enriched in cell adhesion, nervous system function, and synapses in BMN/Ctrl and BM/Ctrl; some were further enriched in BMN/BM. In addition, some of the innate immunity, translation, signal transduction, nervous system, and redox processes were mainly downregulated in BMN/BM. The PRM successfully verified 22 significant DEPs. Among them, UAB1, MTPN, ARHGDIB, IGHG3, and AMBP could be combined to distinguish BMN from BM, achieving an AUC of 0.998 in the training set and 0.824 in the validation set.

Conclusions: This study identified distinct CSF protein expression profiles in children with BMN, BM, and Ctrl, potentially enhancing our understanding of the molecular mechanisms underlying bacterial meningitis. These protein signatures help us distinguish bacterial meningitis from the Ctrl group. Furthermore, selected biomarkers could support the differentiation between BMN and BM.

Background: Four-week dawn-to-dusk dry fasting (DDDF) was previously shown to have a potent anti-inflammatory effect and induce an anti-tumorigenic proteome in the serum and peripheral blood mononuclear cells in subjects without cancer. The study goal was to determine if serum obtained from these subjects without cancer who underwent 4-week DDDF has an anti-tumorigenic effect.

Methods: HepG2 cells were treated with serum collected from four individuals with metabolic syndrome and metabolic dysfunction-associated steatotic liver disease (MASLD) and four healthy individuals who performed 4-week DDDF. The objective was to assess cell proliferation/viability in HepG2 cells treated with non-fasted and dry-fasted serum and determine proteomic changes in human serum. We comparatively performed 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT) cell proliferation assay and untargeted proteomic analysis using nano ultra-high performance liquid chromatography coupled with tandem mass spectrometry.

Results: Serum collected from 3 out of 4 subjects with metabolic syndrome and MASLD at the end of 4-week DDDF (dry-fasted serum/V2) significantly reduced proliferation/viability in HepG2 cells compared with the serum collected before 4-week DDDF (non-fasted serum/V1). A similar reduction effect on cell proliferation was not observed when HepG2 cells were treated with dry-fasted serum collected from healthy subjects. In addition to the in vitro changes observed, the following circulating gene protein products (GP) demonstrated significant increases or decreases in subjects with metabolic syndrome and MASLD after a 4-week DDDF regimen, compared with their GP levels before the 4-week DDDF: CD248 molecule (mean log2 fold = 8.124, P = 0.001), dipeptidyl peptidase 4 (mean log2 fold = 0.937, P = 0.027), lymphatic vessel endothelial hyaluronan receptor 1 (mean log2 fold = 1.054, P = 0.029), LDL receptor related protein 1 (mean log2 fold = 1.401, P = 0.031), and beta-2-microglobulin (mean log2 fold= -0.977, P = 0.033) at the end of 4-week DDDF compared with the GP levels before 4-week DDDF.

Conclusion: This study demonstrated that dry-fasted serum collected from subjects with metabolic syndrome and MASLD decreased HepG2 cell proliferation in vitro and showed that proteomic changes occurred in vivo. These findings suggest that DDDF may be an effective intervention for inducing proteomic responses that could assist in the prevention and adjunct treatment of cancers associated with metabolic syndrome.

Background: The treatment of advanced or metastatic colorectal cancer (CRC) poses a global challenge. Mendelian Randomization (MR) has been primarily applied for repurposing licensed drugs and uncovering new therapeutic targets.

Objective: This study aims to systematically identify potential plasma protein targets for CRC using proteome-wide Mendelian randomization and evaluate their potential side effects through phenome-wide association studies (Phe-WAS).

Methods: We conducted a comprehensive proteome-wide MR study to assess the causal relationships between plasma proteins and the risk of CRC and evaluate their potential side effects through Phe-WAS. The plasma proteins were sourced from the Finland and Iceland decode database, encompassing GWAS data for plasma proteins (Olink-619 samples across 2925 proteins, SomaScan -828 samples across 7596 proteins and Iceland decode database across 4907 proteins). Additionally, GWAS data for CRC were extracted from the UK Biobank-SAIGE database, including 3051 cases and 382,756 controls. Subsequently, colocalization analysis was performed to identify shared causal variants between plasma proteins and CRC. Finally, a phenome-wide association study (Phe-WAS) was conducted to examine the potential adverse effects of druggable proteins for CRC, utilizing the extensive UK Biobank-SAIGE database, encompassing 783 phenotypes.

Results: The MR analysis identified GREM1, DKKL1, and CHRDL2 as plasma proteins whose genetically predicted levels were positively associated with CRC risk, whereas TMEM132A was inversely associated with CRC risk (P_fdr < 0.05). The colocalization analysis identified these four proteins as shared variation with CRC (PPH3 + PPH4 > 0.7), suggesting that these proteins represent potential direct targets for CRC intervention. Further phenotype-wide association studies showed no significant potential side effects of these targets (P_fdr > 0.05).

Conclusion: This proteome-wide Mendelian randomization study offers a comprehensive molecular landscape of CRC, identifying GREM1, DKKL1, CHRDL2, and TMEM132A as potential therapeutic targets. Our research provides a critical foundation for future experimental validation and therapeutic development in colorectal cancer management.

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.