Abstract：
:Hepatocellular carcinoma (HCC) causes more than half a million annual deaths worldwide. Understanding the mechanisms contributing to HCC development is highly desirable for improved surveillance, diagnosis, and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC development. Also, it allows identification of biomarker candidates for future evaluation in biofluids and investigation of racial disparities in HCC. Tumor and nontumor tissues from 40 patients were analyzed by both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) platforms to increase the metabolome coverage. The levels of the metabolites extracted from solid liver tissue of the HCC area and adjacent non-HCC area were compared. Among the analytes detected by GC-MS and LC-MS with significant alterations, 18 were selected based on biological relevance and confirmed metabolite identification. These metabolites belong to TCA cycle, glycolysis, purines, and lipid metabolism and have been previously reported in liver metabolomic studies where high correlation with HCC progression is implied. We demonstrated that metabolites related to HCC pathogenesis can be identified through liver tissue metabolomic analysis. Additionally, this study has enabled us to identify race-specific metabolites associated with HCC.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Ferrarini A,Di Poto C,He S,Tu C,Varghese RS,Kara Balla A,Jayatilake M,Li Z,Ghaffari K,Fan Z,Sherif ZA,Kumar D,Kroemer A,Tadesse MG,Ressom HWdoi
10.1021/acs.jproteome.9b00185subject
Has Abstractpub_date
2019-08-02 00:00:00pages
3067-3076issue
8eissn
1535-3893issn
1535-3907journal_volume
18pub_type
杂志文章abstract：:Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200323a
更新日期：2011-10-07 00:00:00
abstract：:Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To ide...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00460
更新日期：2017-10-06 00:00:00
abstract：:Various mammalian cells including tumor cells secrete extracellular vesicles (EVs), otherwise known as exosomes and microvesicles. EVs are nanosized bilayered proteolipids and play multiple roles in intercellular communication. Although many vesicular proteins have been identified, their functional interrelationships ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200842h
更新日期：2012-02-03 00:00:00
abstract：:Protein or peptide sample losses could accompany all steps of the proteomic analysis workflow. We focused on suppression of sample adsorptive losses during sample storage in autosampler vials. We examined suppression capabilities of six different sample injection solutions and seven types of autosampler vial surfaces ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400183v
更新日期：2013-06-07 00:00:00
abstract：:NMR ligand affinity screening is a powerful technique that is routinely used in drug discovery or functional genomics to directly detect protein-ligand binding events. Binding events can be identified by monitoring differences in the 1D (1)H NMR spectrum of a compound with and without protein. Although a single NMR sp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00121
更新日期：2016-04-01 00:00:00
abstract：:Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8001113
更新日期：2008-09-01 00:00:00
abstract：:The characterization of the humoral response in Alzheimer's disease (AD) patients might aid in detecting the disease at early stages. We have combined phage display and protein microarrays to identify AD autoantibodies and their target biomarkers. After enrichment of the T7 phage display libraries from AD and healthy ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00258
更新日期：2019-07-05 00:00:00
abstract：:Recent advances in genome editing technologies have enabled the insertion of epitope tags at endogenous loci with relative efficiency. We describe an approach for investigation of protein interaction dynamics of the AMP-activated kinase complex AMPK using a catalytic subunit AMPKα2 (PRKAA2 gene) as the bait, based on ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00378
更新日期：2019-10-04 00:00:00
abstract：:Ozonated autohemotherapy (O3-AHT) is a medical approach during which blood obtained from the patient is ozonated and injected back into the body. Despite an increasing number of evidence that O3-AHT is safe, this type of therapy remains controversial. To extend knowledge about the changes in blood evoked by O3-AHT, LC...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3008946
更新日期：2012-12-07 00:00:00
abstract：:Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070491n
更新日期：2008-01-01 00:00:00
abstract：:InterMetalDB is a free-of-charge database and browser of intermolecular metal binding sites that are present on the interfaces of macromolecules forming larger assemblies based on structural information deposited in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00906
更新日期：2021-01-27 00:00:00
abstract：:Deamidation of asparaginyl residues in proteins produces a mixture of asparaginyl, n-aspartyl, and isoaspartyl residues, which affects the proteins' structure, function, and stability. Thus, it is important to identify and quantify the products to evaluate the effects in biological systems. It is still a challenging t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr201048c
更新日期：2012-03-02 00:00:00
abstract：:Biomarkers for colorectal cancer (CRC) early diagnosis are currently lacking. The purpose of this study was to interpret molecular events in the early stage of CRC that may bring about new biomarkers for early diagnosis. Methylation isotope labeling assistant gel-enhanced liquid chromatography-mass spectrometry (GeLC-...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100406z
更新日期：2010-09-03 00:00:00
abstract：:We present a novel straightforward method for enrichment of N-terminal peptides, utilizing charge-based fractional diagonal chromatography (ChaFRADIC). Our method is robust, easy to operate, fast, specific, and more sensitive than existing methods, enabling the differential quantitation of 1459 nonredundant N-terminal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400435d
更新日期：2013-09-06 00:00:00
abstract：:A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00516
更新日期：2017-11-03 00:00:00
abstract：:The development of medical interventions for the preservation of disease-free longevity would be facilitated by markers that predict healthy aging. Altered protein N-glycosylation patterns have been found with increasing age and several disease states. Here we investigate whether glycans derived from the total glycopr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1009959
更新日期：2011-04-01 00:00:00
abstract：:Quantifying peptides based on unique peptide fragment ions avoids the issue of ratio distortion that is commonly observed for reporter ion-based quantification approaches. Herein, we present a collision-induced dissociation-cleavable, isobaric acetyl-isoleucine-proline-glycine (Ac-IPG) tag, which conserves the merits ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00371
更新日期：2020-09-04 00:00:00
abstract：:Many neurodegenerative diseases, such as Parkinson's disease, can be directly correlated with the deregulation in neuronal signaling. Hence, it is indispensable for therapy development to understand the participating signaling processes. Because the activity of the involved protein kinases is of major interest for the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500163r
更新日期：2014-08-01 00:00:00
abstract：:Compartment proteomics enable broad characterization of target tissues. We employed a simple fractionation method and filter-aided sample preparation (FASP) to characterize the cytosolic and membrane fractions of white perch ovary tissues by semiquantitative tandem mass spectrometry using label-free quantitation based...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401067g
更新日期：2014-03-07 00:00:00
abstract：:HER2-testing in breast and gastric cancers is mandatory for the treatment with trastuzumab. We hypothesized that imaging mass spectrometry (IMS) of breast cancers may be useful for generating a classifier that may determine HER2-status in other cancer entities irrespective of primary tumor site. A total of 107 breast ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100573s
更新日期：2010-12-03 00:00:00
abstract：:High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, w...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00419
更新日期：2015-08-07 00:00:00
abstract：:The purpose of this study was to determine the system-wide consequences of deficiencies in two essential micronutrients, vitamins E and C, on the proteome using zebrafish (Danio rerio) as one of the few vertebrate models that similar to humans cannot synthesize vitamin C. We describe a label-free proteomics workflow t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401108d
更新日期：2014-03-07 00:00:00
abstract：:The skin is the primary boundary between the body and the environment. In addition to its properties as a physical barrier, skin keratinocytes actively participate in many defense mechanisms. Viral double-stranded RNA (dsRNA) is the most important viral structure involved in activation of immune response. Intracellula...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr901040u
更新日期：2010-03-05 00:00:00
abstract：:Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress response...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00474
更新日期：2017-10-06 00:00:00
abstract：:Vascular endothelial growth factor receptor-2 (VEGFR-2) is an important receptor tyrosine kinase (RTK) that plays critical roles in both physiologic and pathologic angiogenesis. The extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains, each with multiple potential N-glycosylation sites (seq...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00738
更新日期：2017-02-03 00:00:00
abstract：:Mammary tumors are a major health threat to women and female dogs. In both, metastasis of the primary tumor to distant organs is the most common cause of tumor-related death. Nevertheless, the molecular mechanisms of tumor metastasis are far from being understood, and it is still unknown why some human and canine carc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100671c
更新日期：2010-12-03 00:00:00
abstract：:Recombinant virus-like particles (VLPs) have been shown to induce protective immunity. Despite their potential significance as promising vaccine candidates, the protein composition of VLPs produced in insect cells has not been well characterized. Here we report a proteomic analysis of influenza VLPs containing hemaggl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200086v
更新日期：2011-08-05 00:00:00
abstract：:Protein phosphorylation is essential for numerous cellular processes. Large-scale profiling of phosphoproteins continues to enhance the depth and speed at which we understand these processes. The development of effective phosphoprotein and peptide enrichment techniques and improvements to mass spectrometric instrument...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060559j
更新日期：2007-03-01 00:00:00
abstract：:The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501039k
更新日期：2015-05-01 00:00:00
abstract：:Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00106
更新日期：2016-07-01 00:00:00
