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https://www.readbyqxmd.com/read/27847095/proteomic-analysis-and-translational-perspective-of-hepatocellular-carcinoma-identification-of-diagnostic-protein-biomarkers-by-an-onco-proteogenomics-approach
#1
REVIEW
Shyh-Horng Chiou, King-Teh Lee
Hepatocellular carcinoma (HCC) has been ranked as the third leading cause of cancer-related mortality worldwide. Typically, patients are already in advanced stages of liver cirrhosis at the time of HCC diagnosis. Because HCC is often detected at a late stage and is highly aggressive, noninvasive biomarkers are urgently needed for early diagnosis. Recent advances in gene-expression profiling technologies have enabled molecular classification of HCC into defined subclasses that provide a firm basis for further study of potential mechanisms and biomarkers underlying the development of HCC...
November 2016: Kaohsiung Journal of Medical Sciences
https://www.readbyqxmd.com/read/27846794/genome-and-catabolic-subproteomes-of-the-marine-nutritionally-versatile-sulfate-reducing-bacterium-desulfococcus-multivorans-dsm-2059
#2
Marvin Dörries, Lars Wöhlbrand, Michael Kube, Richard Reinhardt, Ralf Rabus
BACKGROUND: Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27843720/proteogenomic-analyses-indicate-bacterial-methylotrophy-and-archaeal-heterotrophy-are-prevalent-below-the-grass-root-zone
#3
Cristina N Butterfield, Zhou Li, Peter F Andeer, Susan Spaulding, Brian C Thomas, Andrea Singh, Robert L Hettich, Kenwyn B Suttle, Alexander J Probst, Susannah G Tringe, Trent Northen, Chongle Pan, Jillian F Banfield
Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10-20 cm and 30-40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate...
2016: PeerJ
https://www.readbyqxmd.com/read/27815279/comparative-proteogenomics-and-metabolic-profiling-identify-an-inducible-operon-involved-in-inulin-utilization-in-lactobacillus-plantarum-strains
#4
Nirunya Buntin, Tipparat Hongpattarakere, Jarmo Ritari, François P Douillard, Lars Paulin, Sjef Boeren, Sudarshan A Shetty, Willem M de Vos
: The draft genome of L. plantarum isolated from Asian fermented foods, infant feces and shrimp intestines were sequenced and compared to those of well-studied strains. Among twenty-eight strains of L. plantarum, the variation of genomic features involved in the ecological adaptation were elucidated. The genome sizes ranged from approximately 3.1 to 3.5 Mb, of which about 2,932 to 3,345 of protein-coding sequences (CDS) were predicted. The food derived isolates contained higher number of carbohydrate metabolism associated genes than those from infant feces...
November 4, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27807831/quantitative-clinical-imaging-methods-for-monitoring-intratumoral-evolution
#5
Joo Yeun Kim, Robert A Gatenby
Solid tumors are multiscale, open, complex, dynamic systems: complex because they have many interacting components, dynamic because both the components and their interactions can change with time, and open because the tumor freely communicates with surrounding and even distant host tissue. Thus, it is not surprising that striking intratumoral variations are commonly observed in clinical imaging such as MRI and CT and that several recent studies found striking regional variations in the molecular properties of cancer cells from the same tumor...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27807744/computational-methods-in-mass-spectrometry-based-proteomics
#6
Sujun Li, Haixu Tang
This chapter introduces computational methods used in mass spectrometry-based proteomics, including those for addressing the critical problems such as peptide identification and protein inference, peptide and protein quantification, characterization of posttranslational modifications (PTMs), and data-independent acquisitions (DIA). The chapter concludes with emerging applications of proteomic techniques, such as metaproteomics, glycoproteomics, and proteogenomics.
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27797325/-adar-mediated-messenger-rna-editing-analysis-at-the-proteome-level
#7
REVIEW
A A Kliuchnikova, K G Kuznetsova, S A Moshkovskii
Post-transcriptional RNA editing by RNA specific adenosine deaminases (ADAR) was discovered more than two decades ago. It provides additional regulation of animal and human transcriptome. In most cases, it occurs in nervous tissue, where, as a result of the reaction, adenosine is converted to inosine in particular sites of RNA. In case of messenger RNA, during translation, inosine is recognized as guanine leading to amino acid substitutions. Those substitutions are shown to affect substantially the function of proteins, e...
July 2016: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/27786492/a-flexible-data-analysis-pipeline-for-high-confidence-proteogenomics
#8
Hendrik Weisser, James C Wright, Jonathan M Mudge, Petra Gutenbrunner, Jyoti S Choudhary
Proteogenomics leverages information derived from proteomic data in order to improve genome annotations. Of particular interest are "novel" peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such "novel" peptides in proteomic datasets. This pipeline implements criteria developed by proteomics and genome annotation experts for high-stringency peptide identification and filtering...
October 27, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27785359/pygeno-a-python-package-for-precision-medicine-and-proteogenomics
#9
Tariq Daouda, Claude Perreault, Sébastien Lemieux
pyGeno is a python package mainly intended for precision medicine applications that revolve around genomics and proteomics. It integrates reference sequences and annotations from Ensembl, genomic polymorphisms from the dbSNP database and data from next-gen sequencing into an easy to use, memory-efficient and fast framework, therefore allowing the user to easily explore subject-specific genomes and proteomes. Compared to a standalone program, pyGeno gives the user access to the complete expressivity of python, a general programming language...
2016: F1000Research
https://www.readbyqxmd.com/read/27775698/nitrogen-fixation-in-a-chemoautotrophic-lucinid-symbiosis
#10
Sten König, Olivier Gros, Stefan E Heiden, Tjorven Hinzke, Andrea Thürmer, Anja Poehlein, Susann Meyer, Magalie Vatin, Didier Mbéguié-A-Mbéguié, Jennifer Tocny, Ruby Ponnudurai, Rolf Daniel, Dörte Becher, Thomas Schweder, Stephanie Markert
The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO2 and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont-host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy)...
October 24, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27775567/a-proteogenomic-approach-to-understanding-myc-function-in-metastatic-medulloblastoma-tumors
#11
Jerome A Staal, Yanxin Pei, Brian R Rood
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease...
October 19, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27775198/mapping-the-triticum-aestivum-proteome
#12
Owen Duncan, Josua Trösch, Ricarda Fenske, Nicolas L Taylor, A Harvey Millar
Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27734975/a-proteogenomic-approach-for-protein-level-evidence-of-genomic-variants-in-cancer-cells
#13
Jeonghun Yeom, Mohammad Humayun Kabir, Byungho Lim, Hee-Sung Ahn, Seon-Young Kim, Cheolju Lee
Variations in protein coding sequence may sometimes play important roles in cancer development. However, since variants may not express into proteins due to various cellular quality control systems, it is important to get protein-level evidence of the genomic variations. We present a proteogenomic strategy getting protein-level evidence of genomic variants, which we call sequential targeted LC-MS/MS based on prediction of peptide pI and Retention time (STaLPIR). Our approach shows improved peptide identification, and has the potential for the unbiased analysis of variant sequence as well as corresponding reference sequence...
October 13, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27686811/proteogenomics-for-the-comprehensive-analysis-of-human-cellular-and-serum-antibody-repertoires
#14
Paula Díez, Manuel Fuentes
The vast repertoire of immunoglobulins produced by the immune system is a consequence of the huge amount of antigens to which we are exposed every day. The diversity of these immunoglobulins is due to different mechanisms (including VDJ recombination, somatic hypermutation, and antigen selection). Understanding how the immune system is capable of generating this diversity and which are the molecular bases of the composition of immunoglobulins are key challenges in the immunological field. During the last decades, several techniques have emerged as promising strategies to achieve these goals, but it is their combination which appears to be the fruitful solution for increasing the knowledge about human cellular and serum antibody repertoires...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686810/proteogenomics-for-the-study-of-gastrointestinal-stromal-tumors
#15
Tadashi Kondo
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. Gain-of-function mutations in KIT or platelet-derived growth factor receptor alpha (PDGFRA) drive most GISTs, and 85 % of GISTs also contain oncogenic mutations in one of two receptor tyrosine kinases. The advent of tyrosine kinase inhibitors has had a significant impact on the clinical practices for GISTs. However, tumors in more than 80 % of GIST patients acquire resistance against treatments with tyrosine kinase inhibitors; thus, driver mechanisms of secondary resistance as well as biomarkers for early detection of recurrence have been explored for better clinical outcomes...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686809/developments-for-personalized-medicine-of-lung-cancer-subtypes-mass-spectrometry-based-clinical-proteogenomic-analysis-of-oncogenic-mutations
#16
Toshihide Nishimura, Haruhiko Nakamura
Molecular therapies targeting lung cancers with mutated epidermal growth factor receptor (EGFR) by EGFR-tyrosin kinase inhibitors (EGFR-TKIs), gefitinib and erlotinib, changed the treatment system of lung cancer. It was revealed that drug efficacy differs by race (e.g., Caucasians vs. Asians) due to oncogenic driver mutations specific to each race, exemplified by gefitinib / erlotinib. The molecular target drugs for lung cancer with anaplastic lymphoma kinase (ALK) gene translocation (the fusion gene, EML4-ALK) was approved, and those targeting lung cancers addicted ROS1, RET, and HER2 have been under development...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686808/proteogenomic-analysis-of-single-amino-acid-polymorphisms-in-cancer-research
#17
Alba Garin-Muga, Fernando J Corrales, Victor Segura
The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686807/mutant-proteogenomics
#18
Ákos Végvári
Identification of mutant proteins in biological samples is one of the emerging areas of proteogenomics. Despite the fact that only a limited number of studies have been published up to now, it has the potential to recognize novel disease biomarkers that have unique structure and desirably high specificity. Such properties would identify mutant proteoforms related to diseases as optimal drug targets useful for future therapeutic strategies. While mass spectrometry has demonstrated its outstanding analytical power in proteomics, the most frequently applied bottom-up strategy is not suitable for the detection of mutant proteins if only databases with consensus sequences are searched...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686806/using-proteomics-bioinformatics-tools-and-resources-in-proteogenomic-studies
#19
Marc Vaudel, Harald Barsnes, Helge Ræder, Frode S Berven
Proteogenomic studies ally the omic fields related to gene expression into a combined approach to improve the characterization of biological samples. Part of this consists in mining proteomics datasets for non-canonical sequences of amino acids. These include intergenic peptides, products of mutations, or of RNA editing events hypothesized from genomic, epigenomic, or transcriptomic data. This approach poses new challenges for standard peptide identification workflows. In this chapter, we present the principles behind the use of peptide identification algorithms and highlight the major pitfalls of their application to proteogenomic studies...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27686805/identification-of-small-novel-coding-sequences-a-proteogenomics-endeavor
#20
Volodimir Olexiouk, Gerben Menschaert
The identification of small proteins and peptides has consistently proven to be challenging. However, technological advances as well as multi-omics endeavors facilitate the identification of novel small coding sequences, leading to new insights. Specifically, the application of next generation sequencing technologies (NGS), providing accurate and sample specific transcriptome / translatome information, into the proteomics field led to more comprehensive results and new discoveries. This book chapter focuses on the inclusion of RNA-Seq and RIBO-Seq also known as ribosome profiling, an RNA-Seq based technique sequencing the +/- 30 bp long fragments captured by translating ribosomes...
2016: Advances in Experimental Medicine and Biology
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