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https://www.readbyqxmd.com/read/28528867/a-pan-cancer-proteogenomic-atlas-of-pi3k-akt-mtor-pathway-alterations
#1
Yiqun Zhang, Patrick Kwok-Shing Ng, Melanie Kucherlapati, Fengju Chen, Yuexin Liu, Yiu Huen Tsang, Guillermo de Velasco, Kang Jin Jeong, Rehan Akbani, Angela Hadjipanayis, Angeliki Pantazi, Christopher A Bristow, Eunjung Lee, Harshad S Mahadeshwar, Jiabin Tang, Jianhua Zhang, Lixing Yang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman, Lovelace J Luquette, Ruibin Xi, Lynda Chin, Alexei Protopopov, Thomas F Westbrook, Carl Simon Shelley, Toni K Choueiri, Michael Ittmann, Carter Van Waes, John N Weinstein, Han Liang, Elizabeth P Henske, Andrew K Godwin, Peter J Park, Raju Kucherlapati, Kenneth L Scott, Gordon B Mills, David J Kwiatkowski, Chad J Creighton
Molecular alterations involving the PI3K/AKT/mTOR pathway (including mutation, copy number, protein, or RNA) were examined across 11,219 human cancers representing 32 major types. Within specific mutated genes, frequency, mutation hotspot residues, in silico predictions, and functional assays were all informative in distinguishing the subset of genetic variants more likely to have functional relevance. Multiple oncogenic pathways including PI3K/AKT/mTOR converged on similar sets of downstream transcriptional targets...
May 8, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#2
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28513289/detection-of-meat-species-adulteration-using-high-resolution-mass-spectrometry-and-a-proteogenomics-strategy
#3
Alberto Ruiz Orduna, Erik Husby, Charles T Yang, Dipankar Ghosh, Francis Beaudry
Due to the internationalization of food production and distribution, there has been a significant increase of food fraud in recent years. Food fraud can have serious health implications, and occurs when food manufacturers implement unethical practices such as making false label claims as well as using additives and fillers within their products to increase profitability. This has been a serious concern. Meat adulteration was examined using a well-defined proteogenomic annotation, carefully selected surrogate tryptic peptides and high-resolution mass spectrometry...
May 17, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28512450/host-plant-compatibility-shapes-the-proteogenome-of-frankia-coriariae
#4
Amir Ktari, Abdellatif Gueddou, Imen Nouioui, Guylaine Miotello, Indrani Sarkar, Faten Ghodhbane-Gtari, Arnab Sen, Jean Armengaud, Maher Gtari
Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles in establishing the rhizosphere microbiome. RE are known to induce the secretion by rhizobia of Nod factors, polysaccharides, and other proteins in the case of legume symbiosis. Next-generation proteomic approach was here used to decipher the key bacterial signals matching the first-step recognition of host plant stimuli upon treatment of Frankia coriariae strain BMG5...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28456751/methods-tools-and-current-perspectives-in-proteogenomics
#5
Kelly V Ruggles, Karsten Krug, Xiaojing Wang, Karl R Clauser, Jing Wang, Samuel H Payne, David Fenyö, Bing Zhang, D R Mani
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e., the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease...
April 29, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28452485/systematic-comparison-of-false-discovery-rate-controlling-strategies-for-proteogenomic-search-using-spike-in-experiments
#6
Honglan Li, Jonghun Park, Hyunwoo Kim, Kyu-Baek Hwang, Eunok Paek
Proteogenomic searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated, however, mainly due to the difficulty in confirming the existence of identified novel peptides. We simulated a proteogenomic search using a controlled, spike-in proteomic data set. After confirming that the results of the simulated proteogenomic search were similar to those of a real proteogenomic search using a human cell line data set, we evaluated the performance of six FDR control methods-global, separate, and multistage FDR estimation, respectively, coupled to a target-decoy search and a mixture model-based method-on novel peptide identification...
May 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28452122/identification-of-sequence-variants-within-experimentally-validated-protein-interaction-sites-provides-new-insights-into-molecular-mechanisms-of-disease-development
#7
Blaz Skrlj, Janez Konc, Tanja Kunej
Protein interactions (PI) underlie complex biological processes. Protein interaction partners include DNA, RNA, ions, small chemical compounds, and proteins (protein-protein interactions; PPI). Analysis of sequence variants within regions corresponding to experimentally validated PI sites presents novel opportunities for understanding of complex diseases. Such information has not been systematically collected due to the fact that datasets are dispersed throughout databases and publications. Sequence variants and PI regions were obtained from the UniProt database...
April 28, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28440318/corrigendum-proteogenomic-integration-reveals-therapeutic-targets-in-breast-cancer-xenografts
#8
Kuan-Lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P Gunawardena, Kelly V Ruggles, D R Mani, Karl R Clauser, Maki Tanioka, Jerry Usary, Shyam M Kavuri, Ling Xie, Christopher Yoon, Jana W Qiao, John Wrobel, Matthew A Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E Snider, Jeremy Hoog, Purba Singh, Beifang Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D McLellan, Michael C Wendl, Anna Malovannaya, Jason M Held, Michael A Gillette, David Fenyö, Christopher R Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R Davies, Charles M Perou, Cynthia Ma, R Reid Townsend, Xian Chen, Steven A Carr, Matthew J Ellis, Li Ding
No abstract text is available yet for this article.
April 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28436007/overexpression-of-the-regulatory-subunit-of-glutamate-cysteine-ligase-enhances-monoclonal-antibody-production-in-cho-cells
#9
Camila A Orellana, Esteban Marcellin, Peter P Gray, Lars K Nielsen
For decades, Chinese hamster ovary (CHO) cells have been the preferred host for therapeutic monoclonal antibody (mAb) production; however, increasing mAb titer by rational engineering remains a challenge. Our previous proteomic analysis in CHO cells suggested that a higher content of glutathione (GSH) might be related to higher productivity. GSH is an important antioxidant, cell detoxifier, and is required to ensure the formation of native disulfide bonds in proteins. To investigate the involvement of GSH in mAb production, we generated stable CHO cell lines overexpressing genes involved in the first step of GSH synthesis; namely the glutamate-cysteine ligase catalytic subunit (Gclc) and the glutamate-cysteine ligase modifier subunit (Gclm)...
April 24, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#10
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28407323/proteogenomic-analysis-reveals-alternative-splicing-and-translation-as-part-of-the-abscisic-acid-response-in-arabidopsis-seedlings
#11
Fu-Yuan Zhu, Mo-Xian Chen, Neng-Hui Ye, Lu Shi, Kai-Long Ma, Jing-Fang Yang, Yun-Ying Cao, Youjun Zhang, Takuya Yoshida, Alisdair R Fernie, Guang-Yi Fan, Bo Wen, Ruo Zhou, Tie-Yuan Liu, Tao Fan, Bei Gao, Di Zhang, Ge-Fei Hao, Shi Xiao, Ying-Gao Liu, Jianhua Zhang
In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues. However, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment...
April 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28382042/proteogenomic-analysis-greatly-expands-the-identification-of-proteins-related-to-reproduction-in-the-apogamous-fern-dryopteris-affinis-ssp-affinis
#12
Jonas Grossmann, Helena Fernández, Pururawa M Chaubey, Ana E Valdés, Valeria Gagliardini, María J Cañal, Giancarlo Russo, Ueli Grossniklaus
Performing proteomic studies on non-model organisms with little or no genomic information is still difficult. However, many specific processes and biochemical pathways occur only in species that are poorly characterized at the genomic level. For example, many plants can reproduce both sexually and asexually, the first one allowing the generation of new genotypes and the latter their fixation. Thus, both modes of reproduction are of great agronomic value. However, the molecular basis of asexual reproduction is not well understood in any plant...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28348404/proteogenomic-integration-reveals-therapeutic-targets-in-breast-cancer-xenografts
#13
Kuan-Lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P Gunawardena, Kelly V Ruggles, D R Mani, Karl R Clauser, Maki Tanioka, Jerry Usary, Shyam M Kavuri, Ling Xie, Christopher Yoon, Jana W Qiao, John Wrobel, Matthew A Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E Snider, Jeremy Hoog, Purba Singh, Beifung Niu, Zhanfang Guo, Sam Qiancheng Sun, Souzan Sanati, Emily Kawaler, Xuya Wang, Adam Scott, Kai Ye, Michael D McLellan, Michael C Wendl, Anna Malovannaya, Jason M Held, Michael A Gillette, David Fenyö, Christopher R Kinsinger, Mehdi Mesri, Henry Rodriguez, Sherri R Davies, Charles M Perou, Cynthia Ma, R Reid Townsend, Xian Chen, Steven A Carr, Matthew J Ellis, Li Ding
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases...
March 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/28347863/common-bean-proteomics-present-status-and-future-strategies
#14
Sajad Majeed Zargar, Reetika Mahajan, Muslima Nazir, Preeti Nagar, Sun Tae Kim, Vandna Rai, Antonio Masi, Syed Mudasir Ahmad, Riaz Ahmad Shah, Nazir Ahmad Ganai, Ganesh K Agrawal, Randeep Rakwal
Common bean (Phaseolus vulgaris L.) is a legume of appreciable importance and usefulness worldwide to the human population providing food and feed. It is rich in high-quality protein, energy, fiber and micronutrients especially iron, zinc, and pro-vitamin A; and possesses potentially disease-preventing and health-promoting compounds. The recently published genome sequence of common bean is an important landmark in common bean research, opening new avenues for understanding its genetics in depth. This legume crop is affected by diverse biotic and abiotic stresses severely limiting its productivity...
March 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28317871/insights-into-molecular-therapy-of-glioma-current-challenges-and-next-generation-blueprint
#15
REVIEW
Y Rajesh, Ipsita Pal, Payel Banik, Sandipan Chakraborty, Sachin A Borkar, Goutam Dey, Ahona Mukherjee, Mahitosh Mandal
Glioma accounts for the majority of human brain tumors. With prevailing treatment regimens, the patients have poor survival rates. In spite of current development in mainstream glioma therapy, a cure for glioma appears to be out of reach. The infiltrative nature of glioma and acquired resistance substancially restrict the therapeutic options. Better elucidation of the complicated pathobiology of glioma and proteogenomic characterization might eventually open novel avenues for the design of more sophisticated and effective combination regimens...
May 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/28317375/comparison-of-false-discovery-rate-control-strategies-for-variant-peptide-identifications-in-shotgun-proteogenomics
#16
Mark V Ivanov, Anna A Lobas, Dmitry S Karpov, Sergei A Moshkovskii, Mikhail V Gorshkov
Proteogenomic studies aiming at identification of variant peptides using customized database searches of mass spectrometry data are facing a dilemma of selecting the most efficient database search strategy: A choice has to be made between using combined or sequential searches against reference (wild-type) and mutant protein databases or directly against the mutant database without the wild-type one. Here we called these approaches "all-together", "one-by-one", and "direct", respectively. We share the results of the comparison of these search strategies obtained for large data sets of publicly available proteogenomic data...
May 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28286965/harnessing-the-power-of-proteomics-for-identification-of-oncogenic-druggable-signalling-pathways-in-cancer
#17
Heather C Murray, Matthew D Dun, Nicole M Verrills
Genomic and transcriptomic profiling of tumours has revolutionised our understanding of cancer. However, the majority of tumours possess multiple mutations, and determining which oncogene, or even which pathway, to target is difficult. Proteomics is emerging as a powerful approach to identify the functionally important pathways driving these cancers, and how they can be targeted therapeutically. Areas covered: The authors provide a technical overview of mass spectrometry based approaches for proteomic profiling, and review the current and emerging strategies available for the identification of dysregulated networks, pathways, and drug targets in cancer cells, with a key focus on the ability to profile cancer kinomes...
March 17, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28276747/proteogenomic-studies-on-cancer-drug-resistance-towards-biomarker-discovery-and-target-identification
#18
Shuyue Fu, Xiang Liu, Maochao Luo, Ke Xie, Edouard C Nice, Haiyuan Zhang, Canhua Huang
Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment...
March 6, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28271730/recent-mass-spectrometry-based-proteomics-for-biomarker-discovery-in-lung-cancer-copd-and-asthma
#19
Kiyonaga Fujii, Haruhiko Nakamura, Toshihide Nishimura
Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made it possible to analyze disease-relevant proteins expressed in clinical specimens by proteomic challenges. Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches...
April 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28187513/collaboration-to-accelerate-proteogenomics-cancer-care-the-department-of-veterans-affairs-department-of-defense-and-the-national-cancer-institute-s-applied-proteogenomics-organizational-learning-and-outcomes-apollo-network
#20
REVIEW
L D Fiore, H Rodriguez, C D Shriver
A tri-federal initiative arising out of the Cancer Moonshot has resulted in the formation of a program to utilize advanced genomic and proteomic expression platforms on high-quality human biospecimens in near-real-time in order to identify potentially actionable therapeutic molecular targets, study the relationship of molecular findings to cancer treatment outcomes, and accelerate novel clinical trials with biomarkers of prognostic and predictive value.
May 2017: Clinical Pharmacology and Therapeutics
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