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https://www.readbyqxmd.com/read/28620443/pattern-recognition-for-predictive-preventive-and-personalized-medicine-in-cancer
#1
REVIEW
Tingting Cheng, Xianquan Zhan
Predictive, preventive, and personalized medicine (PPPM) is the hot spot and future direction in the field of cancer. Cancer is a complex, whole-body disease that involved multi-factors, multi-processes, and multi-consequences. A series of molecular alterations at different levels of genes (genome), RNAs (transcriptome), proteins (proteome), peptides (peptidome), metabolites (metabolome), and imaging characteristics (radiome) that resulted from exogenous and endogenous carcinogens are involved in tumorigenesis and mutually associate and function in a network system, thus determines the difficulty in the use of a single molecule as biomarker for personalized prediction, prevention, diagnosis, and treatment for cancer...
March 2017: EPMA Journal
https://www.readbyqxmd.com/read/28618245/multi-omics-integrative-investigation-of-fatty-acid-metabolism-in-obese-and-lean-subcutaneous-tissue
#2
Flavia Badoud, Dyanne Brewer, Armen Charchoglyan, Daniel J Cuthbertson, David M Mutch
White adipose tissue (WAT) plays a central role in whole-body energy homeostasis through storage and release of fatty acids. A deeper understanding of the complex and highly integrated pathways regulating WAT fatty acid metabolism, and how they are altered with obesity, is necessary for diagnostic and therapeutic innovations in nutritional disorders. In this multi-omics study, we investigated the influence of obesity on fatty acid metabolism in human subcutaneous adipose tissue (SAT) using an approach that integrated transcriptomic, peptidomic, and fatty acid analyses...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28603764/data-on-endogenous-bovine-ovarian-follicular-cells-peptides-and-small-proteins-obtained-through-top-down-high-resolution-mass-spectrometry
#3
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
The endogenous peptides and small proteins extracted from bovine ovarian follicular cells (oocytes, cumulus and granulosa cells) were identified by Top-down High Resolution Mass Spectrometry (TD-HR-MS/MS) in order to annotate peptido- and proteoforms detected using qualitative and quantitative profiling method based on ICM-MS (Intact Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). The description and analysis of these Top-down MS data in the context of oocyte quality biomarkers research are available in the original research article of Labas et al...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28598000/peptidomic-analysis-of-maternal-serum-to-identify-biomarker-candidates-for-prenatal-diagnosis-of-tetralogy-of-fallot
#4
Bin Zhuang, Yin Hu, Xuemei Fan, Mengmeng Li, Jingai Zhu, Heng Liu, Li Cao, Dong Liang, Jingjing Zhang, Zhangbin Yu, Shuping Han
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease. To identify endogenous peptides possibly involved in the progression of TOF, we performed comparative peptidomic profiling of maternal serum between normal fetuses and fetuses suffering from TOF. A total of 278 differentially expressed peptides, including 94 over-expressed peptides and 184 under-expressed peptides, originating from 227 protein precursors were identified by Liquid Chromatography/Mass Spectrometry (LC/MS) in maternal serum of fetuses with TOF compared to normal controls...
June 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28594947/mass-spectrometry-based-serum-peptidome-profiling-accurately-and-reliably-predicts-outcomes-of-pemetrexed-plus-platinum-chemotherapy-in-patients-with-advanced-lung-adenocarcinoma
#5
Lin Wang, Chuanhao Tang, Bin Xu, Lin Yang, Lili Qu, Liangliang Li, Xiaoyan Li, Weixia Wang, Haifeng Qin, Hongjun Gao, Kun He, Xiaoqing Liu
BACKGROUND: Although pemetrexed plus cis/carboplatin has become the most effective chemotherapy regimen for patients with advanced lung adenocarcinoma, predictive biomarkers are not yet available, and new tools to identify chemosensitive patients who would likely benefit from this treatment are desperately needed. In this study, we constructed and validated predictive peptide models using the serum peptidome profiles of two datasets. METHODS: One hundred eighty-three patients treated with first-line platinum-based pemetrexed treatment for advanced lung adenocarcinoma were retrospectively enrolled and randomized into the training (n = 92) or validation (n = 91) set, and pre-treatment serum samples were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and ClinProTools software...
2017: PloS One
https://www.readbyqxmd.com/read/28588123/a-genoproteomic-approach-to-detect-peptide-markers-of-bacterial-respiratory-pathogens
#6
Honghui Wang, Steven K Drake, Chen Yong, Marjan Gucek, Matthew A Lyes, Avi Z Rosenberg, Erik Soderblom, M Arthur Moseley, John P Dekker, Anthony F Suffredini
BACKGROUND: Rapid identification of respiratory pathogens may facilitate targeted antimicrobial therapy. Direct identification of bacteria in bronchoalveolar lavage (BAL) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is confounded by interfering substances. We describe a method to identify unique peptide markers of 5 gram-negative bacteria by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for direct pathogen identification in BAL. METHODS: In silico translation and digestion were performed on 14-25 whole genomes representing strains of Acinetobacter baumannii, Moraxella catarrhalis, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Klebsiella pneumoniae...
June 6, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28566732/peptide-markers-for-rapid-detection-of-kpc-carbapenemase-by-lc-ms-ms
#7
Honghui Wang, Steven K Drake, Jung-Ho Youn, Avi Z Rosenberg, Yong Chen, Marjan Gucek, Anthony F Suffredini, John P Dekker
Carbapenemase producing organisms (CPOs) represent an urgent public health threat, and the need for new rapid methods to detect these organisms has been widely recognized. CPOs carrying the Klebsiella pneumoniae carbapenemase (bla KPC ) gene have caused outbreaks globally with substantial attributable mortality. Here we describe the validation of a rapid MS method for the direct detection of unique tryptic peptides of the KPC protein in clinical bacterial isolates with an isolate-to-result time of less than 90 minutes...
May 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514659/the-intergenic-recombinant-hla-b%C3%A2-46-01-has-a-distinctive-peptidome-that-includes-kir2dl3-ligands
#8
Hugo G Hilton, Curtis P McMurtrey, Alex S Han, Zakia Djaoud, Lisbeth A Guethlein, Jeroen H Blokhuis, Jason L Pugh, Ana Goyos, Amir Horowitz, Rico Buchli, Ken W Jackson, Wilfred Bardet, David A Bushnell, Philip J Robinson, Juan L Mendoza, Michael E Birnbaum, Morten Nielsen, K Christopher Garcia, William H Hildebrand, Peter Parham
HLA-B(∗)46:01 was formed by an intergenic mini-conversion, between HLA-B(∗)15:01 and HLA-C(∗)01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B(∗)46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B(∗)46:01 has a low-diversity peptidome that is distinct from those of its parents...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28490095/a-cold-induced-phytosulfokine-peptide-is-related-to-the-improvement-of-loquat-fruit-chilling-tolerance
#9
Huwei Song, Xinfeng Wang, Weicheng Hu, Xianghui Yang, Enjie Diao, Ting Shen, Qian Qiang
A novel peptidomics approach was used to discover cold-induced peptides in loquat fruit. Twenty unique peptides derived from 18 proproteins were identified, and they were involved in sugar signalling, protein metabolism and stress response. The quantitative analysis revealed 7 peptides with more than 2-fold upregulation, especially a 4.96-fold increase detected in the phytosulfokine (PSK) peptide. To further evaluate effects of PSK1 on fruit chilling tolerance, weight loss, firmness and internal browning were investigated in PSK1-treated loquat fruit at 0°C...
October 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28482090/p4p-a-peptidome-based-strain-level-genome-comparison-web-tool
#10
Aitor Blanco-Míguez, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny...
May 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28474961/urine-peptidomic-biomarkers-for-diagnosis-of-patients-with-systematic-lupus-erythematosus
#11
M Pejchinovski, J Siwy, W Mullen, H Mischak, M A Petri, L C Burkly, R Wei
Background Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery...
January 1, 2017: Lupus
https://www.readbyqxmd.com/read/28473704/cancerpdf-a-repository-of-cancer-associated-peptidome-found-in-human-biofluids
#12
Sherry Bhalla, Ruchi Verma, Harpreet Kaur, Rajesh Kumar, Salman Sadullah Usmani, Suresh Sharma, Gajendra P S Raghava
CancerPDF (Cancer Peptidome Database of bioFluids) is a comprehensive database of endogenous peptides detected in the human biofluids. The peptidome patterns reflect the synthesis, processing and degradation of proteins in the tissue environment and therefore can act as a gold mine to probe the peptide-based cancer biomarkers. Although an extensive data on cancer peptidome has been generated in the recent years, lack of a comprehensive resource restrains the facility to query the growing community knowledge...
May 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28460924/a-peptidomic-approach-for-the-identification-of-antioxidant-and-ace-inhibitory-peptides-in-sardinelle-protein-hydrolysates-fermented-by-bacillus-subtilis-a26-and-bacillus-amyloliquefaciens-an6
#13
Ines Jemil, Leticia Mora, Rim Nasri, Ola Abdelhedi, Maria-Concepción Aristoy, Mohamed Hajji, Moncef Nasri, Fidel Toldrá
Antioxidant and angiotensin I-converting enzyme (ACE)-inhibitory activities of sardinelle (Sardinella aurita) protein hydrolysates (SPHs) obtained by fermentation with Bacillus subtilis A26 (SPH-A26) and Bacillus amyloliquefaciens An6 (SPH-An6) were investigated. Both hydrolysates showed dose-dependent antioxidant activities evaluated using various in vitro antioxidant assays. Further, they were found to exhibit ACE-inhibitory activity. Peptides from SPH-A26 and SPH-An6 were analyzed by nESI-LC-MS/MS and approximately 800 peptides were identified...
November 2016: Food Research International
https://www.readbyqxmd.com/read/28456018/unique-features-in-the-presentation-of-insulin-epitopes-in-autoimmune-diabetes-an-update
#14
REVIEW
Xiaoxiao Wan, Emil R Unanue
Although an autoimmune disease involves diverse self-antigens, the initiation stage may require recognition of a limited number. This concept is verified in the non-obese diabetic (NOD) mouse model of autoimmune diabetes, in which strong evidence points to insulin as the prime antigen. The NOD mouse bears the I-A(g7) class II-MHC molecules (MHCII) that share common biochemical features and peptidome selection with the human diabetes-susceptible HLA-DQ8. Furthermore, both NOD mice and patients with type 1 diabetes (T1D) display an early appearance of insulin autoantibodies (IAAs) and subsequent insulin-reactive T cell infiltration into the islets...
April 26, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28453489/changes-of-cerebrospinal-fluid-peptides-due-to-tauopathy
#15
Petra Majerova, Peter Barath, Alena Michalicova, Stanislav Katina, Michal Novak, Andrej Kovac
Alzheimer's disease (AD) and progressive supranuclear palsy are two common neurodegenerative tauopathies, and the most common cause of progressive brain dementia in elderly affecting more than 35 million people. The tauopathies are characterized by abnormal deposition of microtubule associated protein tau into intracellular neurofibrillary tangles composed mainly of the hyperphosphorylated form of the protein. The diagnosis of tauopathies is based on the presence of clinical features and pathological changes...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28446606/the-beh%C3%A3-et-s-disease-associated-variant-of-the-aminopeptidase-erap1-shapes-a-low-affinity-hla-b-51-peptidome-by-differential-subpeptidome-processing
#16
Pablo Guasp, Eilon Barnea, M Francisca González-Escribano, Anaïs Jiménez-Reinoso, José R Regueiro, Arie Admon, José A López de Castro
A low-activity variant of endoplasmic reticulum aminopeptidase 1 (ERAP1), Hap10, is associated with the autoinflammatory disorder Behçet's disease (BD) in epistasis with HLA-B*51, which is the main risk factor for this disorder. The role of Hap10 in BD pathogenesis is unknown. We sought to define the effects of Hap10 on the HLA-B*51 peptidome and to distinguish these effects from those due to HLA-B*51 polymorphisms unrelated to disease. The peptidome of the BD-associated HLA-B*51:08 subtype expressed in a Hap10-positive cell line was isolated, characterized by mass spectrometry, and compared with the HLA-B*51:01 peptidome from cells expressing more active ERAP1 allotypes...
June 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28438560/longitudinal-investigation-of-salivary-proteomic-profiles-in-the-development-of-early-childhood-caries
#17
Shuang Ao, Xiangyu Sun, Xiangru Shi, Xin Huang, Feng Chen, Shuguo Zheng
OBJECTIVES: To investigate differentially expressed salivary peptides in the development of early childhood caries (ECC) in 3-4 year-old children. MATERIALS AND METHODS: Eighty-two caries-free children at baseline were followed-up for 1year, during which period 15 of them had developed ECC (Group C), whilst another 15 cases out of the 31 individuals who remained healthy were marked as Group H. Stimulated whole saliva samples were collected at 0, 6 and 12 months, and analyzed using weak cation exchange magnetic beads combined with matrix assisted laser desorption/ionization time-of-flight mass spectrometry...
April 22, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28435107/wasp-venomic-unravelling-the-toxins-arsenal-of-polybia-paulista-venom-and-its-potential-pharmaceutical-applications
#18
REVIEW
Amilcar Perez-Riverol, José Roberto Aparecido Dos Santos-Pinto, Alexis Musacchio Lasa, Mario Sergio Palma, Márcia Regina Brochetto-Braga
Polybia paulista (Hymenoptera: Vespidae) is a neotropical social wasp from southeast Brazil. As most social Hymenoptera, venom from P. paulista comprises a complex mixture of bioactive toxins ranging from low molecular weight compounds to peptides and proteins. Several efforts have been made to elucidate the molecular composition of the P. paulista venom. Data derived from proteomic, peptidomic and allergomic analyses has enhanced our understanding of the whole envenoming process caused by the insect sting...
April 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28430386/peptidome-analysis-of-human-serum-from-normal-and-preeclamptic-pregnancies
#19
Xiaonan Dai, Xuejing Song, Can Rui, Li Meng, Xuan Xue, Hongjuan Ding, Rong Shen, Jun Li, Jingyun Li, Yuanqing Lu, Wei Long
Preeclampsia is a kind of disease that severely harms the health of pregnant women and infants. To better understand the molecular mechanisms involved in preeclampsia, we used liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) to construct a comparative peptidomic profiling of human serum between normal and preeclamptic pregnancies. A total of 201 peptides were confidently identified, with 21 up-regulated and 3 down-regulated. Further analysis indicated that these differentially expressed peptides correlate with enzyme regulator activity, biological regulation, and coagulation cascades occurring during pathological changes of preeclampsia...
April 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28424255/analysis-of-milk-from-mothers-who-delivered-prematurely-reveals-few-changes-in-proteases-and-protease-inhibitors-across-gestational-age-at-birth-and-infant-postnatal-age
#20
Veronique Demers-Mathieu, Søren Drud Nielsen, Mark A Underwood, Robyn Borghese, David C Dallas
Background: Peptidomics research has demonstrated that protease activity is higher in breast milk from preterm-delivering mothers than from term-delivering mothers. However, to our knowledge, the effect of the degree of prematurity and postnatal age on proteases and protease inhibitors in human milk remains unknown.Objective: We aimed to determine the change of proteases and protease inhibitors in milk from mothers who delivered prematurely across gestational age (GA) and postnatal age.Methods: Milk samples were collected from 18 mothers aged 26-40 y who delivered preterm infants and who lacked mastitis...
June 2017: Journal of Nutrition
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