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Anil K Madugundu, Chan Hyun Na, Raja Sekhar Nirujogi, Santosh Renuse, Kwang Pyo Kim, Kathleen H Burns, Christopher Wilks, Ben Langmead, Shannon E Ellis, Leonardo Collado-Torres, Marc K Halushka, Min-Sik Kim, Akhilesh Pandey
Understanding the molecular profile of every human cell type is essential for understanding its role in normal physiology and disease. Technological advancements in DNA sequencing, mass spectrometry and computational methods allow us to carry out multi-Omics analyses although such approaches are not routine yet. Human umbilical vein endothelial cells (HUVECs) are a widely-used model system to study pathological and physiological processes associated with the cardiovascular system. In this study, we employed next generation sequencing and high-resolution mass spectrometry to profile the transcriptome and proteome of primary HUVECs...
April 14, 2019: Proteomics
Jennifer Guergues, Ping Zhang, Bin Liu, Stanley M Stevens
Microglia, as the resident brain immune cells, can exhibit a broad range of activation phenotypes, which have been implicated in a multitude of central nervous system disorders. Current widely studied microglial cell lines are mainly derived from neonatal rodent brain which can limit their relevance to homeostatic function and disease-related neuroimmune responses in the adult brain. Recently, an adult mouse brain-derived microglial cell line was established; however, a comprehensive proteome dataset remains lacking...
April 12, 2019: Proteomics
Anne D Rocheleau, Alexander R Melrose, Jennifer M Cunliffe, John Klimek, Özgün Babur, Samuel Tassi Yunga, Anh T P Ngo, Jiaqing Pang, Larry L David, Owen J T McCarty, Joseph E Aslan
Protein post-translational modifications critically regulate a range of physiological and disease processes. In addition to tyrosine, serine and threonine phosphorylation, reversible N-ε acylation and alkylation of protein lysine residues also modulate diverse aspects of cellular function. Studies of lysine acyl and alkyl modifications have focused on nuclear proteins in epigenetic regulation; however, lysine modifications are also prevalent on cytosolic proteins to serve increasingly apparent, although less understood roles in cell regulation...
April 11, 2019: Proteomics
Coralie Petit, Jordan Guillon, Bertrand Toutain, Alice Boissard, Anne Patsouris, Eric Lelièvre, Catherine Guette, Olivier Coqueret
In primary cells, senescence induces a permanent proliferative arrest to prevent the propagation of malignant cells. However, the outcome of senescence is more complex in advanced cancer cells where senescent states are heterogeneous. Here, we discuss this heterogeneity and propose that proteomic analysis should be used to identify specific signatures of cancer cells that use this pathway as an adaptative mechanism. Since senescent cells produce an inflammatory secretome, MRM approaches and quantification with internal standards might be particularly suited to follow the expression of the corresponding markers in body fluids...
April 10, 2019: Proteomics
Muhammad Shahid, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L Kim, Jayoung Kim
Metabolic alterations in prostate cancer (PC) are associated with progression and aggressiveness. However, the underlying mechanisms behind PC metabolic functions are unknown. Our group recently reported on the important role of centromere protein F (CENPF), a protein associated with the centromere-kinetochore complex and chromosomal segregation during mitosis, in PC MRI visibility. In this study, we focused on discerning the role of CENPF in metabolic perturbation in human PC3 cells. A series of bioinformatics analyses showed that CENPF is one gene that is strongly associated with aggressive PC, and that its expression is positively correlated with metastasis...
April 8, 2019: Proteomics
Pascal Jézéquel, Catherine Guette, Hamza Lasla, Wilfried Gouraud, Alice Boissard, Catherine Guérin-Charbonnel, Mario Campone
Heterogeneity and lack of targeted therapies represent the two main impediments to precision treatment of triple-negative breast cancer (TNBC). Therefore, molecular subtyping and identification of therapeutic pathways are required to optimize medical care. The aim of the present study was to define robust TNBC subtypes with clinical relevance by means of proteomics and transcriptomics. As a first step, unsupervised analyses were conducted in parallel on proteomics and transcriptomics data of 83 TNBC tumors...
April 5, 2019: Proteomics
Feng Zhu, Fan Zhang, Maxwell Hincke, Zhong-Tao Yin, Si-Rui Chen, Ning Yang, Zhuo-Cheng Hou
The avian egg is a valuable model for the calcitic biomineralization process as it is the fastest calcification process occurring in nature and is a clear example of biomineralization. In this study, we used iTRAQ MS/MS to detect and study for the first time: 1) the overall duck eggshell proteome; 2) regional differences in the proteome between the inner and outer portions of the duck eggshell. The new reference protein datasets allowed us to identify 179 more eggshell proteins than solely using the current release of Ensembl duck annotations...
April 5, 2019: Proteomics
Ashish Kumar, Biswapriya B Misra
Challenges in metabolomics for a given spectrum of disease are more or less comparable, ranging from the accurate measurement of metabolite abundance, compound annotation, identification of unknown constituents, and interpretation of untargeted and analysis of high throughput targeted metabolomics data leading to the identification of biomarkers. However, metabolomics approaches in cancer studies specifically suffer from several additional challenges and require robust ways to sample the cells and tissues in order to tackle the constantly evolving cancer landscape...
April 5, 2019: Proteomics
Taixue An, Sihua Qin, Dehua Sun, Yiyao Huang, Yanwei Hu, Shaopeng Li, Han Zhang, Bo Li, Bo Situ, Linmiao Lie, Yingsong Wu, Lei Zheng
Extracellular vesicles (EVs) mediate intercellular communication via transferring proteins and other biological molecules and have been recently investigated as biomarkers of disease. Sensitive and specific biomarkers are required for lung cancer diagnosis and prognosis. The present study screened for abnormal EV proteins in non-small cell lung cancer (NSCLC) using a quantitative proteomics strategy involving LC-MS/MS to identify ideal biomarkers for NSCLC diagnosis. EVs were enriched from the sera of early and advanced NSCLC patients and healthy controls and from cell culture supernatants of lung adenocarcinoma and bronchial epithelial cell lines...
April 5, 2019: Proteomics
Fuhao Zhang, Hong Song, Min Zeng, Yaohang Li, Lukasz Kurgan, Min Li
Annotation of protein functions plays an important role in understanding life at the molecular level. High throughput sequencing produces massive numbers of raw proteins sequences and only about 1% of them have been manually annotated with functions. Experimental annotations of functions are expensive, time-consuming and do not keep up with the rapid growth of the sequence numbers. This motivates development of computational approaches that predict protein functions. We propose a novel deep learning framework, DeepFunc, which accurately predicts protein functions from protein sequence- and network-derived information...
April 2, 2019: Proteomics
Viktor Brovkovych, Alyssa Aldrich, Nasi Li, G Ekin Atilla-Gokcumen, Jonna Frasor
The use of cultured cells has been instrumental in studying biochemical, molecular, and cellular processes. The composition of serum that cells are maintained in can have a profound impact on important cellular checkpoints. We have analyzed cell growth and apoptosis in an estrogen receptor positive breast cancer cell line in the presence of serum that have been treated to remove steroids or lipids, as well-described in the literature. We showed that maintaining cells in the presence of charcoal-dextran-treated serum causes reduced growth rate, which can be reversed by the addition of estradiol...
March 27, 2019: Proteomics
Rachel Carnes, James A Mobley, David K Crossman, Hui Liu, Bruce R Korf, Robert A Kesterson, Deeann Wallis
Loss of NF1 is an oncogenic driver. In efforts to define pathways responsible for the development of neurofibromas and other cancers, we evaluated transcriptomic and proteomic changes in a non-malignant NF1 null cell line. We created NF1 null HEK293 cells using CRISPR/Cas9 technology and compared them to parental cells that express neurofibromin. We found 1222 genes and 132 proteins to be differentially expressed. We integrated the analysis to identify eight transcripts/proteins that are differentially regulated in both analyses...
March 25, 2019: Proteomics
Aleksey Y Ogurtsov, Gelio Alves, Yi-Kuo Yu
Mass spectrometry based proteomics starts with identifications of peptides and proteins, which provide the bases for forming the next-level hypotheses whose "validations" are often employed for forming even higher level hypotheses and so forth. Scientifically meaningful conclusions are thus attainable only if the number of falsely identified peptides/proteins is accurately controlled. For this reason, we continue to develop RAId in the past decade. RAId employs rigorous statistics for peptides/proteins identification, hence assigning accurate P-values/E-values that can be used confidently to control the number of falsely identified peptides and proteins...
March 25, 2019: Proteomics
Lingna Xu, Lijun Shi, Lin Liu, Ruobing Liang, Qian Li, Jianguo Li, Bo Han, Dongxiao Sun
In this study, we investigated the proteomes of liver tissues in three periods of the lactation cycle of Holstein cows by using isobaric tag for relative and absolute quantification (iTRAQ) technique to obtain liver proteome and identify functional proteins/genes involved with milk synthesis in dairy cattle. Based on iTRAQ analysis, we detected 3,252 proteins in the liver tissues (false discovery rate (FDR) ≤ 0.01). We identified 32 differently expressed proteins (DEPs) among the three periods by p-value < 0...
March 23, 2019: Proteomics
Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Salovska, Yansheng Liu
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, we performed gene knockout of HMGN1 by CRISPR in cancer cells and studied the following proteomic regulation events. In particular, we utilized DIA mass spectrometry (DIA-MS) and reproducibly measured more than 6200 proteins (protein- FDR 1%) and more than 82,000 peptide precursors in the single MS shots of two hours...
March 22, 2019: Proteomics
Yan Li, Yiwei Cheng, Tianyu Zhu, Hao Zhang, Wen Li, Yueshuai Guo, Yaling Qi, Xu Chen, Jun Zhang, Jiahao Sha, Zuomin Zhou, Hui Zhu, Xuejiang Guo
The characteristic tadpole-shape of sperm is formed from round spermatids via spermiogenesis, a process which results in dramatic morphological changes in the final stage of spermatogenesis in the testis. Protein phosphorylation, as one of the most important post-translational modifications, can regulate spermiogenesis; however, the phosphorylation events taking place during this process have not been systematically analyzed. In order to better understand the role of phosphorylation in spermiogenesis, we performed large-scale phosphoproteome profiling using IMAC and TiO2 enrichment...
March 22, 2019: Proteomics
Aikaterini Emmanouilidi, Dino Paladin, David W Greening, Marco Falasca
Exosomes are small extracellular membrane vesicles important in intercellular communication, with their oncogenic cargo attributed in tumour progression and pre-metastatic niche formation. To gain an insight into key differences in oncogenic composition of exosomes we utilised human non-malignant epithelial and pancreatic cancer cell models and purified and characterised resultant exosome populations. Proteomic analysis revealed the selective enrichment of known exosome markers and signalling proteins in comparison to parental cells...
March 20, 2019: Proteomics
Yunqi Wu, Mehdi Mirzaei, Dana Pascovici, Paul A Haynes, Brian J Atwell
Plants require a distinctive cohort of enzymes to coordinate cell division and expansion. Proteomic analysis now enables interrogation of immature leaf bases where these processes occur. Hence we investigated proteins in tissues sampled from leaves of a drought-tolerant rice (IAC1131) to provide insights into the effect of soil drying on gene expression relative to the drought-sensitive genotype Nipponbare. Shoot growth zones were dissected to estimate the proportion of dividing cells and extract protein for subsequent Tandem Mass Tags (TMT) quantitative proteomic analysis...
March 19, 2019: Proteomics
Giovanni C Forcina, Scott J Dixon
Oxygen is necessary for aerobic metabolism but can also contribute to the harmful oxidation of lipids and other macromolecules. Oxidation of cholesterol and of phospholipids containing polyunsaturated fatty acyl chains can lead to lipid peroxidation, membrane damage and cell death. Lipid hydroperoxides are key intermediates in the process of lipid peroxidation. The lipid hydroperoxidase glutathione peroxidase 4 (GPX4) converts lipid hydroperoxides to lipid alcohols, and this process prevents the iron (Fe2+ )-dependent formation of toxic lipid reactive oxygen species (ROS)...
March 19, 2019: Proteomics
Melissa R Pergande, Thu T A Nguyen, Carol Haney-Ball, Cristin D Davidson, Stephanie M Cologna
Niemann-Pick Disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system. This abnormal accumulation results in a cascade of pathophysiological events including progressive, cerebellar neurodegeneration, among others. While significant progress has been made to better understand NPC1, the downstream effects of cholesterol storage and the major mechanisms that drive neurodegeneration remain unclear...
March 19, 2019: Proteomics
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