Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “PROTEOMICS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources
PubMed2004

Proteomic approaches to studying drug targets and resistance in Plasmodium.

Ever increasing drug resistance by Plasmodium falciparum, the most virulent of human malaria parasites, is creating new challenges in malaria chemotherapy. The entire genome sequences of P. falciparum and the rodent malaria parasite, P. yoelii yoelii are now available. Extensive genome sequence data from other Plasmodium species including another important human malaria parasite, P. vivax are also available. Powerful research techniques coupled to genomic resources are needed to help identify new drug and vaccine targets against malaria. Applied to Plasmodium, proteomics combines high-resolution protein or peptide separation with mass spectrometry and computer software to rapidly identify large numbers of proteins expressed from various stages of parasite development. Proteomic methods can be applied to study sub-cellular localization, cell function, organelle composition, changes in protein expression patterns in response to drug exposure, drug-protein binding and validation of data from genomic annotation and transcript expression studies. Recent high-throughput proteomic approaches have provided a wealth of protein expression data on P. falciparum, while smaller-scale studies examining specific drug-related hypotheses are also appearing. Of particular interest is the study of mechanisms of action and resistance of drugs such as the quinolines, whose targets currently may not be predictable from genomic data. Coupling the Plasmodium sequence data with bioinformatics, proteomics and RNA transcript expression profiling opens unprecedented opportunities for exploring new malaria control strategies. This review will focus on pharmacological research in malaria and other intracellular parasites using proteomic techniques, emphasizing resources and strategies available for Plasmodium.

Animals↗
PubMed2026

Cross-ancestry proteome-wide Mendelian randomization prioritizes 12 plasma protein candidates for breast cancer risk.

The plasma proteome provides a molecular bridge between genetic variation and disease risk, yet its contribution to breast cancer susceptibility across ancestries remains unclear. We conducted a proteome-wide Mendelian randomization (MR) study of 2,923 plasma proteins using cis-protein quantitative trait loci from 34,557 European participants in the UK Biobank Pharma Proteomics Project, integrated with genome-wide association studies of 156,901 breast cancer cases and 204,634 controls of European, East Asian, and African ancestries. Cross-ancestry meta-analysis identified 12 candidate proteins associated with breast cancer risk (P < 2.5&#xd7;10-5), including six previously reported and six newly implicated in MR studies. DNPH1 showed cross-ancestry heterogeneity, with a risk-increasing association in European populations and a nominally inverse association in East Asian populations. CASP8, RALB, and USP28 displayed subtype-differentiated associations. Orthogonal validation provided variable support: six demonstrated strong evidence of statistical colocalization; four replicated in an independent European proteomic dataset (deCODE, n = 35,559); two replicated in an independent East Asian proteomic dataset (JCTF, n = 1,384); and four were supported by polygenic-score analyses in the ancestrally diverse All of Us cohort (9,250 cases, 214,857 controls). These findings prioritize a high-confidence subset of plasma proteins, including LRRC25, PARK7, and LRRC37A2, for future mechanistic and translational investigation.

Mendelian randomization↗
PubMed2001

[Progress in proteomics].

Proteomics, the large-scale analysis of proteins, will contribute greatly to our understanding of gene function in the post-genome era. Proteomics uses a combination of sophisticated techniques including two-dimensional(2D) gel electrophoresis, mass spectrometry, yeast two-hybrid system, bioinformatics, etc. to characterize, to quantify, and to analyze cellular proteins in a global way. The application of proteomics provides major opportunities to elucidate disease mechanisms and to identify new therapeutic targets. This review aims to explain the definition of proteomics and then to outline proteomic techniques. Finally, applications to the study of human disease are briefly discussed.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2002

[Proteomics in clinical research: new approach of mass spectrometry].

A proteome has been defined as the protein complement expressed by the genome of an organism, tissue, or differentiated cell. Knowledge of complete genome sequences has led to considerable effort being increasingly devoted to the large-scale study of proteomes, that is, 'proteomics'. Commonly, two proteomes are compared by a substructive analysis in which differences due to drug treatment, culture conditions, genetic variations, or diseases can be observed. Two-dimensional gel electrophoresis and mass spectrometry are commonly used for this purpose. We applied this approach to the analysis of vitreous humor(VH) proteins. Fifty-two different proteins were identified on silver-stained 2D-gel patterns with VH proteins obtained from diabetic retinopathy and macular hole. Thirty-five proteins, which have not reported in plasma, were found in VH. Pigment epithelium-derived factor, which was reported to be a potent inhibitor of angiogenesis in cornea and vitreous was at a higher concentration in VH with diabetes than in that with macular hole. It is impressive that the inhibitor increases in the vitreous with proliferative angiogenesis. Unique applications in proteomics promise a bright future for molecular biology and hopefully for clinical chemistry.

Aqueous Humor↗
PubMed2002

Proteomics in alcohol research.

The proteome is the complete set of proteins in an organism. It is considerably larger and more complex than the genome--the collection of genes that encodes these proteins. Proteomics deals with the qualitative and quantitative study of the proteome under physiological and pathological conditions (e.g., after exposure to alcohol, which causes major changes in numerous proteins of different cell types). To map large proteomes such as the human proteome, proteins from discrete tissues, cells, cell components, or biological fluids are first separated by high-resolution two-dimensional electrophoresis and multidimensional liquid chromatography. Then, individual proteins are identified by mass spectrometry. The huge amount of data acquired using these techniques is analyzed and assembled by fast computers and bioinformatics tools. Using these methods, as well as other technological advances, alcohol researchers can gain a better understanding of how alcohol globally influences protein structure and function, protein-protein interactions, and protein networks. This knowledge ultimately will assist in the early diagnosis and prognosis of alcoholism and the discovery of new drug targets and medications for treatment.

Alcoholism↗
PubMed2004

[Preliminary study on proteomic patterns in hepatic tissue to identify HBV related hepatocellular carcinoma].

OBJECTIVE: To identify proteomic patterns in hepatic tissues for diagnosing early HBV related HCC. METHODS: Proteomic spectra were generated by two-dimensional gel electrophoresis (2-DE), A preliminary "raining" set of spectra derived from analysis of 14 cancer tissues and 14 non-cancer tissues, a proteomic patterns that completely discriminated cancer from non-cancer was identified. The discovered pattern was then used to classify an independent set of 48 masked samples: 24 from cancer tissues, and 24 from non-cancer tissues. RESULTS: The discriminatory pattern correctly identified all cancer tissues and non-cancer tissues in the masked set. This result yielded a sensitivity of 100%, specificity of 100%. CONCLUSION: Further analysis on these proteins in the proteomic pattern will be helpful to screen tumor markers for HBV related HCC. These findings justify a prospective assessment of proteomic pattern technology as a screening tool for cancer in high-risk and general populations.

Carcinoma, Hepatocellular↗
PubMed2004

Proteomics to diagnose human tumors and provide prognostic information.

Proteomics is a rapidly emerging scientific discipline that holds great promise in identifying novel diagnostic and prognostic biomarkers for human cancer. Technologic improvements have made it possible to profile and compare the protein composition within defined populations of cells. Laser capture microdissection is a tool for procuring pure populations of cells from human tissue sections to be used for downstream proteomic analysis. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has been used traditionally to separate complex mixtures of proteins. Improvements in this technology have greatly enhanced resolution and sensitivity providing a more reproducible and comprehensive survey. Image analysis software and robotic instrumentation have been developed to facilitate comparisons of complex protein expression patterns and isolation of differentially expressed proteins spots. Differential in-gel electrophoresis (DIGE) facilitates protein expression by labeling different populations of proteins with fluorescent dyes. Isotope-coded affinity tagging (ICAT) uses mass spectroscopy for protein separation and different isotope tags for distinguishing populations of proteins. Although in the past proteomics has been primarily used for discovery, significant efforts are being made to develop proteomic technologies into clinical tools. Reverse-phase protein arrays offer a robust new method of quantitatively assessing expression levels and the activation status of a panel of proteins. Surface-enhanced laser-desorption/ionization time-of-flight (SELDI-TOF) mass spectroscopy rapidly assesses complex protein mixtures in tissue or serum. Combined with artificial intelligence-based pattern recognition algorithms, this emerging technology can generate highly accurate diagnostic information. It is likely that mass spectroscopy-based serum proteomics will evolve into useful clinical tools for the detection and treatment of human cancers.

Early Diagnosis↗
PubMedDate not supplied

A review of proteomics in cancer research.

The most functional compartment encoded by the genome is proteome. Therefore study of proteome i.e. proteomics is the promising approach in identification, separation and quantitation of functional changes. It aims to gain a comprehensive understanding of the expressions, modifications, interactions, and regulation of proteins in cells. The power of two-dimensional electrophoresis and advances in mass spectrometric techniques, combined with sequence data base correlation, has enabled speed and accuracy in identification of proteins in complex mixtures. Therefore, proteomics may provide a better understanding of the molecular basis of cancer growth, with identification of potential pathological markers and therapeutic targets. Tobacco related cancers are the major health hazard in Asian countries; the proteomics approach should be employed for understanding the underlying disease processes and hopefully reveal important clues for identifying high risk individuals and early changes during malignant transformation.

Biomarkers, Tumor↗
PubMed2005

Proteomics of boar seminal plasma - current studies and possibility of their application in biotechnology of animal reproduction.

Proteomics is critical to identify the properties and functions of proteins involved in the mechanism regulating the male reproductive tract function. This approach is important in male fertility assessment and clinical diagnosis of the physiological state of individual reproductive organs. Proteomics also provides a tool to understand the interactions of seminal plasma proteins with spermatozoa, which could provide a useful model for studying ligand-cell interaction occurring at the sperm cell surface. This review covers a selection of advances in the realm of functional proteomics of boar seminal plasma proteins and is focused on some fundamental proteomic technologies. Also, this review explores key themes in proteomics and their application in animal reproductive techniques.

Animals↗
PubMed2005

Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics.

Shotgun proteomics, where a tryptic digest of a complex proteome sample is directly analyzed by either single dimensional or multidimensional liquid chromatography tandem mass spectrometry, has gained acceptance in the proteomics community at large and is widely used in core facilities. Here we review the development in our laboratory of an alternative first-dimension separation technique for shotgun proteomics, immobilized pH gradient isoelectric focusing (IPG-IEF). The key advantages of the technology over other multidimensional separation formats (simplicity, high resolution, and high sensitivity) are discussed. The concept of using peptide pI to filter large shotgun proteomics datasets generated by the IPG-IEF technique to minimize false positives and negatives is also introduced. Finally, an account of the comparison of the technique with the established gold standard for multidimensional separation of peptides, strong cation exchange chromatography, is presented, along with the prospects for the use of peptide pI along with accurate mass measurement for the identification of peptides.

Chromatography, Ion Exchange↗
PubMedDate not supplied

The evolving role of proteomics in the early detection of breast cancer.

There has been emerging interest in the examination of tumor protein expression (proteomics) as a means to identify novel diagnostic and therapeutic targets in women with breast cancer. Specifically, several investigators have examined biological fluids (serum and breast ductal fluid) and breast tissue in an attempt to detect novel proteomic profiles in women with breast carcinoma. The current tools of proteomic research are evolving, but include two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. Initial studies have identified several unique biomarkers and proteomic profiles that were able to discriminate between non-cancer and breast cancer patients. In the future, the application of large-scale proteomic technology may provide a means of early detection, surveillance, and identification of potential therapeutic targets.

Biomarkers, Tumor↗
PubMed2006

[Exploration on correlation of syndrome proteomics and syndromatology of TCM].

The advent of the Post-Human Genome Project Era, represented by the raising of proteomics, would inevitably lead to the change of molecular biology from topical view to holistic with its thought turning from linear to complex mode. Based on the proteomics development in recent years, the authors summarized the methodology of TCM syndromatologic research, advocated in using two-dimensional gel electrophoresis (2-DE) and bioinformatics to identify different proteins. Proteomics should be led into the research of TCM syndrome categorization and the rule of evolution, which is necessary for researching the integration of the TCM study with proteomics and even with modern molecular biology based on molecular epidemiology level. Owing to the gradually developed coherence and mutual penetration of proteomics and TCM on the thinking method in studying life science, it has denoted the necessity and importance of integration of TCM and Western medicine in investigating the complex vital life phenomena.

Diagnosis, Differential↗
PubMed2006

Proteomic analysis of opsins and thyroid hormone-induced retinal development using isotope-coded affinity tags (ICAT) and mass spectrometry.

PURPOSE: Analyses that reveal the relative abundance of proteins are informative in elucidating mechanisms of retinal development and disease progression. However, popular high-throughput proteomic methods do not reliably detect opsin protein abundance, which serve as markers of photoreceptor differentiation. We utilized thyroid-hormone (TH) treatment of rainbow trout (Oncorhynchus mykiss) as a model of cone apoptosis and cone regeneration. We used this model to investigate if emerging proteomic technology allows effective analysis of retinal development and opsin protein abundance. We also sought to begin a characterization of proteomic changes in the retina occurring with TH treatment and address whether TH affects proliferation or photoreceptor differentiation. METHODS: Retinal homogenates were prepared from control and TH-treated fish. Peptides from control and treated homogenates were differentially labeled, using isotope-code affinity tags (ICAT) and analyzed using capillary liquid chromatography-electrospray ionization-tandem mass spectrometry (capLC-ESI-MS/MS). This method identifies proteins and quantifies their relative abundance between two samples. RESULTS: The relative abundance of many retinal proteins changed during TH treatment. These included proteins from every functional class. We detected 1,684 different peptides, and our quantification suggests that 94 increased and 146 decreased in abundance more than 50% during TH treatment. Cell-cycle proteins appear to be increased, consistent with TH-inducing cell proliferation, similar to its effect in Xenopus. Other proteins associated with retinal development, such as deltaA and tubulins, changed in abundance during TH treatment. Rod opsin and three cone opsins were identified and the relative abundance of each changed with TH treatment. CONCLUSIONS: ICAT and capLC-ESI-MS/MS are an effective complement to other molecular approaches that investigate the mechanisms of retinal development. Unlike other proteomic techniques, this approach does not require development of species- or tissue-specific methodology, such as characterizing two dimensional (2D) gels or antibodies, in order to be practical as a high-throughput approach. Importantly, this technology was able to assess the relative abundance of opsin proteins. These findings represent the first high-throughput proteomic analysis of the retina and demonstrate the technique's ability to provide useful information in retinal development.

Animals↗
PubMed2025

Plasma Proteomic Profiles of Pediatric Patients With Human Herpesvirus 6B Encephalitis Following Umbilical Cord Blood Transplantation.

Human herpesvirus 6B (HHV-6B) encephalitis is a rare but severe complication of hematopoietic cell transplantation. This study investigated the pathogenesis of HHV-6B encephalitis by comparing plasma proteomic profiles of four pediatric patients with HHV-6B encephalitis to three with asymptomatic HHV-6B reactivation following umbilical cord blood transplantation (UCBT). Plasma proteomic profiling was conducted using liquid chromatography-mass spectrometry. Overall, 260 proteins were identified and quantified in plasma samples. At the onset of HHV-6B encephalitis and asymptomatic reactivation, 20 and 24 proteins, respectively, were significantly upregulated compared to their respective pre-onset levels. Of these, 11 proteins were uniquely upregulated in HHV-6B encephalitis. S100-A9 and S100-A8 were the most and second-most upregulated proteins in HHV-6B encephalitis, respectively. Elevated plasma S100A8/A9 heterodimer levels were confirmed via enzyme-linked immunosorbent assay in three of the four patients with HHV-6B encephalitis. Pathway analysis identified neutrophil degranulation as the most enriched category among upregulated proteins in HHV-6B encephalitis. Additionally, proteins related to the protein-lipid complex remodeling pathway were more prominently upregulated in HHV-6B encephalitis than in asymptomatic reactivation. Proteomic analysis revealed distinct plasma protein profiles between HHV-6B encephalitis and asymptomatic HHV-6B reactivation in pediatric UCBT recipients. The inflammatory response mediated by S100A8/A9 proteins may play a critical role in the pathogenesis of HHV-6B encephalitis. These findings indicate that proteomic analysis may provide novel insights into the host response to HHV-6B reactivation and the subsequent development of HHV-6B encephalitis.

Humans↗
PubMed2026

Proteomic profiling of bone for the estimation of post-mortem interval and post-mortem submersion interval: a systematic review.

Accurate estimation of the Post-Mortem Interval (PMI) and Post-Mortem Submersion Interval (PMSI) remains a persistent challenge in forensic science, especially when traditional morphological and entomological methods fail due to advanced decomposition or in aquatic environments. Proteomic profiling of bone tissues has recently emerged as a promising approach, leveraging the predictable degradation patterns of bone proteins to estimate time since death more reliably. This systematic review, conducted in accordance with PRISMA guidelines, analyzed 24 peer-reviewed studies focusing on the application of proteomic techniques to bone tissue for PMI and PMSI estimation. The included studies were evaluated based on sample type, analytical techniques used, identified biomarkers, environmental conditions assessed, and the overall reliability and reproducibility of the findings. The review found that specific bone proteins, particularly collagen, osteocalcin, fetuin-A, etc. exhibited consistent degradation patterns that correlated strongly with elapsed post-mortem time. Cortical bone was identified as a more stable and informative matrix compared to trabecular bone. Mass spectrometry, especially LC-MS/MS, emerged as the predominant analytical technique due to its high sensitivity and accuracy in detecting low-abundance proteins over extended PMIs and PMSIs. However, protein degradation rates were significantly influenced by environmental variables such as temperature, humidity, soil pH, and microbial activity. This review also emphasizes the transformative role of bone proteomics in advancing forensic science while identifying key gaps that must be addressed to achieve global standardization and practical implementation in diverse forensic contexts. The integration of proteomics with other emerging technologies, such as machine learning algorithms and computational modeling, may further enhance the precision of PMI and PMSI estimation in future applications.

Postmortem Changes↗
PubMed2025

Exploring the associations between preen oil bacterial, chemical and proteomic profiles of passerines.

Preen gland bacteria are thought to be the key producers of preen oil components such as chemosignalling molecules including volatile organic compounds (VOCs) and antimicrobial compounds including peptides and antimicrobial VOCs. However, data on the preen oil bacteriome and chemical composition are limited to a small subset of bird species, and the presence of antimicrobial peptides is largely unexplored. Here, we performed an exploratory study to characterize, for the first time, the preen oil chemical and proteomic profiles and to explore the possible contribution of the bacteriome to the production of preen oil VOCs and antimicrobial peptides (bacteriocins) in eight passerine species, each represented by a single individual. Preen oil bacteriome, chemical and proteomic profiles varied among birds. The bacterial profiles were dominated by the genera Streptococcus, Lactococcus, Corynebacterium and Cutibacterium. The chemical profiles mainly consisted of alcohols, ketones and carboxylic acids. The biological functions primarily associated with the proteomic profiles were proteolysis and response to oxidative stress. Although we were unable to explore a direct association between the bacteriome and chemical profiles, the preen oil contained bacteriocin- and VOC-producing bacterial genera capable of producing detected microbially-derived VOCs (mVOCs), the relative abundance of which varied between birds. Riparian species showed the highest chemical diversity and high abundances of putative preen oil mVOC-producing bacteria, which could suggest habitat-specific adaptations. This exploratory study may significantly contribute to the formulation of hypotheses on the potential role of host ecological factors in the variation of preen oil bacterial, chemical and proteomic profiles in passerines.

Animals↗
PubMed2024

Proteomic Characterization of Ubiquitin Carboxyl-Terminal Hydrolase 19 Deficient Cells Reveals a Role for USP19 in the Secretion of Lysosomal Proteins.

Ubiquitin carboxyl-terminal hydrolase 19 (USP19) is a unique deubiquitinase, characterized by multiple variants generated by alternative splicing. Several variants bear a C-terminal transmembrane domain that anchors them to the endoplasmic reticulum. Other than regulating protein stability by preventing proteasome degradation, USP19 has been reported to rescue substrates from endoplasmic reticulum-associated protein degradation in a catalytic-independent manner, promote autophagy, and address proteins to lysosomal degradation via endosomal microautophagy. USP19 has recently emerged as the protein responsible for the unconventional secretion of misfolded proteins including Parkinson's disease-associated protein &#x3b1;-synuclein. Despite mounting evidence that USP19 plays crucial roles in several biological processes, the underlying mechanisms are unclear due to lack of information on the physiological substrates of USP19. Herein, we used high-resolution quantitative proteomics to analyze changes in the secretome and cell proteome induced by the loss of USP19 to identify proteins whose secretion or turnover is regulated by USP19. We found that ablation of USP19 induced significant proteomic alterations both in and out of the cell. Loss of USP19 impaired the release of several lysosomal proteins, including legumain (LGMN) and several cathepsins. In order to understand the underlaying mechanism, we dissected the USP19-regulated secretion of LGMN in several cell types. We found that LGMN was not a deubiquitinase substrate of USP19 and that its USP19-dependent release did not require their direct interaction. LGMN secretion occurred by a mechanism that involved the Golgi apparatus, autophagosome formation, and lysosome function. This mechanism resembled the recently described "lysosomal exocytosis," by which lysosomal hydrolases are secreted, when ubiquitination of p62 is increased in cells lacking deubiquitinases such as USP15 and USP17. In conclusion, our proteomic characterization of USP19 has identified a collection of proteins in the secretome and within the cell that are regulated by USP19, which link USP19 to the secretion of lysosomal proteins, including LGMN.

Humans↗
PubMed2024

Retinal Proteome Profiling of Inherited Retinal Degeneration Across Three Different Mouse Models Suggests Common Drug Targets in Retinitis Pigmentosa.

Inherited retinal degenerations (IRDs) are a leading cause of blindness among the population of young people in the developed world. Approximately half of IRDs initially manifest as gradual loss of night vision and visual fields, characteristic of retinitis pigmentosa (RP). Due to challenges in genetic testing, and the large heterogeneity of mutations underlying RP, targeted gene therapies are an impractical largescale solution in the foreseeable future. For this reason, identifying key pathophysiological pathways in IRDs that could be targets for mutation-agnostic and disease-modifying therapies (DMTs) is warranted. In this study, we investigated the retinal proteome of three distinct IRD mouse models, in comparison to sex- and age-matched wild-type mice. Specifically, we used the Pde6&#x3b2;Rd10 (rd10) and RhoP23H/WT (P23H) mouse models of autosomal recessive and autosomal dominant RP, respectively, as well as the Rpe65-/- mouse model of Leber's congenital amaurosis type 2 (LCA2). The mice were housed at two distinct institutions and analyzed using LC-MS in three separate facilities/instruments following data-dependent and data-independent acquisition modes. This cross-institutional and multi-methodological approach signifies the reliability and reproducibility of the results. The large-scale profiling of the retinal proteome, coupled with in&#xa0;vivo electroretinography recordings, provided us with a reliable basis for comparing the disease phenotypes and severity. Despite evident inflammation, cellular stress, and downscaled phototransduction observed consistently across all three models, the underlying pathologies of RP and LCA2 displayed many differences, sharing only four general KEGG pathways. The opposite is true for the two RP models in which we identify remarkable convergence in proteomic phenotype even though the mechanism of primary rod death in rd10 and P23H mice is different. Our data highlights the cAMP and cGMP second-messenger signaling pathways as potential targets for therapeutic intervention. The proteomic data is curated and made publicly available, facilitating the discovery of universal therapeutic targets for RP.

Animals↗