Integrated transcriptome and proteome analysis reveals brassinosteroid-mediated regulation of cambium initiation and patterning in woody stem.

Abstract Wood formation involves sequential developmental events requiring the coordination of multiple hormones. Brassinosteroids (BRs) play a key role in wood development, but little is known about the cellular and molecular processes that underlie wood formation in tree species. Here, we generated transgenic poplar lines with edited PdBRI1 genes, which are orthologs of Arabidopsis vascular-enriched BR receptors, and showed how inhibition of BR signaling influences wood development at the mRNA and/or proteome level. Six Populus PdBRI1 genes formed three gene pairs, each of which was highly expressed in basal stems. Simultaneous mutation of PdBRI1–1, −2, −3 and − 6, which are orthologs of the Arabidopsis vascular-enriched BR receptors BRI1, BRL1 and BRL3, resulted in severe growth defects. In particular, the stems of these mutant lines displayed a discontinuous cambial ring and patterning defects in derived secondary vascular tissues. Abnormal cambial formation within the cortical parenchyma was also observed in the stems of pdbri1–1;2;3;6. Transgenic poplar plants expressing edited versions of PdBRI1–1 or PdBRI1–1;2;6 exhibited phenotypic alterations in stem development at 4.5 months of growth, indicating that there is functional redundancy among these PdBRI1 genes. Integrated analysis of the transcriptome and proteome of pdbri1–1;2;3;6 stems revealed differential expression of a number of genes/proteins associated with wood development and hormones. Concordant (16%) and discordant (84%) regulation of mRNA and protein expression, including wood-associated mRNA/protein expression, was found in pdbri1–1;2;3;6 stems. This study found a dual role of BRs in procambial cell division and xylem differentiation and provides insights into the multiple layers of gene regulation that contribute to wood formation in Populus.

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Proteome Analysis of Differential Protein Expression in Brain of Rats with Type 1 Diabetes Mellitus

Experimental and Clinical Endocrinology & Diabetes ◽

10.1055/s-0031-1271705 ◽

2011 ◽

Vol 119 (05) ◽

pp. 265-270 ◽

Cited By ~ 4

Author(s):

X. Li ◽

W. Pan ◽

G. Z. Yang ◽

Y. N. Di ◽

F. Zhao ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 1 Diabetes ◽

Protein Expression ◽

Type 1 Diabetes Mellitus ◽

Proteome Analysis ◽

Differential Protein Expression ◽

Differential Protein

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Integrated analysis highlights APC11 protein expression as a likely new independent predictive marker for colorectal cancer

Scientific Reports ◽

10.1038/s41598-018-25631-1 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 6

Author(s):

Youenn Drouet ◽

Isabelle Treilleux ◽

Alain Viari ◽

Sophie Léon ◽

Mojgan Devouassoux-Shisheboran ◽

...

Keyword(s):

Colorectal Cancer ◽

Protein Expression ◽

Predictive Marker ◽

Integrated Analysis

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2D-DIGE A Powerful Tool for Proteome Analysis

Protocols used in Molecular Biology ◽

10.2174/9789811439315120010010 ◽

2020 ◽

pp. 67-73

Keyword(s):

Protein Expression ◽

Gel Electrophoresis ◽

Proteome Analysis ◽

Great Sensitivity ◽

Two Dimensional Gel Electrophoresis ◽

2D Dige ◽

Protein Sample ◽

Different Types ◽

Complex Protein ◽

2D Gel

In the recent past, two dimensional gel electrophoresis has emerged as a powerful molecular biology tool for the comparative expression profiling of complex protein sample. It involves the separation as well as the resolution of diverse proteins sample on the basis of isoelectric points and molecular mass of protein in two dimension ways. In this way, it reflects the view of overall proteome status including differentiation in protein expression levels, post-translational modifications etc. Moreover, this allows the identification of novel biological signatures, which may give a particular identity of pathological background to cells or tissues associated with various types of cancers and neurological disorders. Therefore, by utilizing such tools, one can clearly investigate and compare the effects of particular drugs on cells of tissues and also one can analyze the effects of disease on the basis of variations in protein expression profile at broad spectrum. Recently, to get more error-less and accurate proteome profile, conventional 2-D gel electrophoresis has been enhanced with the inclusion of different types of protein labeling dyes which enables a more comparative analysis of diverse protein sample in a single 2-D gel. In this advanced technique (2-D-DIGE), protein samples are labeled with three different types of CyDyes (Cy2, Cy3, and Cy5) separately and combined and further resolved on the same gel. This will facilitate the more accurate spot matching on a single gel platform and will also minimize the experimental variations as commonly reported in the conventional 2D-gel electrophoresis. Therefore, in the present proteomic research era, 2D-DIGE has proved to be an extremely powerful tool with great sensitivity for up to 125 ng of proteins in clinical research volubility especially, neurological and cancer related disorders.

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Non-bacterial protein expression in periodontal pockets by proteome analysis

Journal Of Clinical Periodontology ◽

10.1111/jcpe.12050 ◽

2013 ◽

Vol 40 (6) ◽

pp. 573-582 ◽

Cited By ~ 19

Author(s):

Carlo Bertoldi ◽

Elisa Bellei ◽

Chiara Pellacani ◽

Davide Ferrari ◽

Andrea Lucchi ◽

...

Keyword(s):

Protein Expression ◽

Proteome Analysis ◽

Bacterial Protein

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Integrated Analysis of PTEN and p4EBP1 Protein Expression as Predictors for pCR in HER2-Positive Breast Cancer

Clinical Cancer Research ◽

10.1158/1078-0432.ccr-15-0965 ◽

2016 ◽

Vol 22 (11) ◽

pp. 2675-2683 ◽

Cited By ~ 26

Author(s):

Sibylle Loibl ◽

Silvia Darb-Esfahani ◽

Jens Huober ◽

Alexander Klimowicz ◽

Jenny Furlanetto ◽

...

Keyword(s):

Breast Cancer ◽

Protein Expression ◽

Integrated Analysis ◽

Her2 Positive ◽

Her2 Positive Breast Cancer ◽

Positive Breast Cancer

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Characterization of Plasmodium falciparum Proteome at Asexual Blood Stages for Screening of Effective Vaccine Candidates: An Immunoinformatics Approach

Immunology and Immunogenetics Insights ◽

10.4137/iii.s24755 ◽

2015 ◽

Vol 7 ◽

pp. III.S24755 ◽

Cited By ~ 5

Author(s):

Satarudra Prakash Singh ◽

Vishal Verma ◽

Bhartendu Nath Mishra

Keyword(s):

Plasmodium Falciparum ◽

T Cell ◽

Cell Epitope ◽

Epitope Prediction ◽

Proteome Analysis ◽

Effective Vaccine ◽

Secretory Proteins ◽

Vaccine Candidates ◽

Proteome Level

Malaria is a complex parasitic disease that is currently causing great concerns globally owing to the resistance to antimalarial drugs and lack of an effective vaccine. The present study involves the characterization of extracellular secretory proteins as vaccine candidates derived from proteome analysis of Plasmodium falciparum at asexual blood stages of malaria. Among the screened 32 proteins, 31 were predicted as antigens by the VaxiJen program, and 26 proteins had less than two transmembrane spanning regions predicted using the THMMM program. Moreover, 10 and 5 proteins were predicted to contain secretory signals by SignalP and TargetP, respectively. T-cell epitope prediction using MULTIPRED2 and NetCTL programs revealed that most of the predicted antigens are immunogenic and contain more than 10% supertype and 5% promiscuous epitopes of HLA-A, -B, or -DR. We anticipate that T-cell immune responses against asexual blood stages of Plasmodium are dispersed on a relatively large number of parasite antigens. This is the first report, to the best of our knowledge, offering new insights, at the proteome level, for the putative screening of effective vaccine candidates against the malaria pathogen. The findings also suggest new ways forward for the modern omics-guided vaccine target discovery using reverse vaccinology.

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Analysis of xylem formation in pine by cDNA sequencing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.95.16.9693 ◽

1998 ◽

Vol 95 (16) ◽

pp. 9693-9698 ◽

Cited By ~ 209

Author(s):

Isabel Allona ◽

Michelle Quinn ◽

Elizabeth Shoop ◽

Kristi Swope ◽

Sheila St. Cyr ◽

...

Keyword(s):

Cell Wall ◽

Loblolly Pine ◽

Secondary Xylem ◽

Expression Patterns ◽

Wood Formation ◽

Xylem Differentiation ◽

Cell Wall Proteins ◽

Powerful Means ◽

Xylem Formation ◽

Enzymes Of Carbohydrate Metabolism

Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (Pinus taeda L.). A total of 1,097 single-pass sequences were obtained from 5′ ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.

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Identification of distinct protein Signatures Associated with genetic Abnormalities In Acute Lymphoblastic Leukemia

Blood ◽

10.1182/blood.v122.21.1313.1313 ◽

2013 ◽

Vol 122 (21) ◽

pp. 1313-1313

Author(s):

Roland P. Kuiper ◽

Blanca Scheijen ◽

Agata Pastorczak ◽

Simon V. van Reijmersdal ◽

Deborah A. Thomas ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Protein Expression ◽

Copy Number ◽

Lymphoblastic Leukemia ◽

Chromosomal Translocation ◽

Genetic Alterations ◽

Chromosomal Translocations ◽

Integrated Analysis ◽

Copy Number Alterations ◽

Protein Signatures

Abstract Background Treatment outcome in acute lymphoblastic leukemia (ALL) has improved over the past 30 years, with overall survival rates of ∼45% in adults and ∼85% in children. Gross cytogenetic abnormalities, including numerical changes and chromosomal translocations, are of considerable prognostic value in both pediatric and adult ALL. In addition, we and others have recently identified novel molecular markers associated with a poor outcome in ALL, including deletions of the lymphoid transcription factor IKZF1. In order to identify downstream signaling events associated with these genetic alterations, we performed an integrated analysis of genomic abnormalities, including copy number alterations, sequence mutations and chromosomal translocations, with alterations in protein expression and modification. Methods A cohort of 91 precursor B-ALL cases treated at M.D. Anderson Cancer Center in Houston, USA, including 82 newly diagnosed cases and 5 diagnosis-relapse pairs was used for this study. The cohort consisted of 6 children (age 1-6), 30 young adults (age 15-39) and 45 adults (age>39), and 20 patients carried a BCR-ABL1 chromosomal translocation. Copy number alterations in eight genes frequently deleted in ALL (IKZF1, PAX5, EBF1, RB1, CRLF2, CDKN2A/2B, BTG1, and ETV6) were determined by multiplex ligation-dependent probe amplification analysis. IKZF1 deletions were associated with relapse (Pearson's chi-square test, p=0.009), and the presence of BCR-ABL1 translocation (p=0.032). Protein expression and modification levels were determined by probing Reverse Phase Protein Arrays (RPPA) containing protein lysates of all above samples with 128 rigorously validated antibodies including 34 phospho-specific antibodies. Hierarchical clustering analysis was used to determine which (phospho)proteins are differently expressed in genetic subsets of ALL. The significance of correlations was determined using two-sample t-test, with correction for multiple testing (Beta-Uniform Mixture model). Results We identified clustering of cases with a BCR-ABL1 chromosomal translocation (p=0.01; false discovery rate (FDR)=0.1), IKZF1-deletions (p=0.01, FDR=0.072), RB1-deletions (p=0.03, FDR=0.43) and EBF1 deletions (p=0.05, FDR=0.63). As expected RB1 deletion positive cases were characterized by decreased levels of (phospho)-RB1 and increased levels of cyclin E, illustrating the validity of our approach. EBF1-deleted cases showed relatively high levels of SHIP1, SSBP2 and phospho-STAT5, and lower levels of FAK and LYN. The protein signatures of BCR-ABL1-positive cases and IKZF1-deletion positive cases largely overlapped, and were characterized by elevated levels of (phospho)PKCα, SMAD1, phospho-STAT3, and phospho-STAT5 and lower levels of LYN and cyclinD3 (Figure 1). In total 70% of the BCR-ABL1-positive cases carried an IKZF1 deletion and several BCR-ABL1-negative cases with similar RPPA signature could be identified, all of which were IKZF1-deletion positive. These cases may represent the “BCR-ABL1-like” cases that were previously identified using gene expression signatures (Mullighan et al. 2009, NEJM 360:470-480; Den Boer et al. 2009, Lancet Oncol. 10:125-134), and could reflect activation of cAbl or other cellular tyrosine kinases. Together, we conclude that integrated analysis of genetic and proteomic aberrations identified protein signatures downstream of recurrent mutational events in ALL, a strategy that promises to facilitate the discovery of novel therapeutic targets in ALL and may aid in the identification of (high risk) patients that would benefit from tyrosine kinase inhibition. Disclosures: No relevant conflicts of interest to declare.

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Rapid Proteome Analysis of Bronchoalveolar Lavage Samples of Lifelong Smokers and Never-Smokers by Micro-Scale Liquid Chromatography and Mass Spectrometry

Clinical Chemistry ◽

10.1373/clinchem.2005.060715 ◽

2006 ◽

Vol 52 (4) ◽

pp. 671-679 ◽

Cited By ~ 43

Author(s):

Amelie Plymoth ◽

Ziping Yang ◽

Claes-Göran Löfdahl ◽

Ann Ekberg-Jansson ◽

Magnus Dahlbäck ◽

...

Keyword(s):

Mass Spectrometry ◽

Liquid Chromatography ◽

Protein Expression ◽

Bronchoalveolar Lavage ◽

Proteomic Analysis ◽

Ion Trap ◽

Wide Spectrum ◽

Proteome Analysis ◽

Chronic Obstructive ◽

Never Smokers

Abstract Background: The aim of this study was to determine whether relative qualitative and quantitative differences in protein expression could be related to smoke exposure or smoke-induced airway inflammation. We therefore explored and characterized the protein components found in bronchoalveolar lavage (BAL) fluid sampled from either lifelong smokers or never-smokers. Methods: BAL fluid samples obtained by bronchoscopy from 60-year-old healthy never-smokers (n = 18) and asymptomatic smokers (n = 30) were analyzed in either pooled or individual form. Initial global proteomic analysis used shotgun digestion approaches on unfractionated BAL fluid samples (after minimal sample preparation) and separation of peptides by gradient (90-min) liquid chromatography (LC) coupled with on-line linear ion trap quadropole mass spectrometry (LTQ MS) for identification and analysis. Results: LTQ MS identified 481 high- to low-abundance proteins. Relative differences in patterns of BAL fluid proteins in smokers compared with never-smokers were observed in pooled and individual samples as well as by 2-dimensional gel analysis. Gene ontology categorization of all annotated proteins showed a wide spectrum of molecular functions and biological processes. Conclusions: The described method provides comprehensive qualitative proteomic analysis of BAL fluid protein expression from never-smokers and from smokers at risk of developing chronic obstructive pulmonary disease. Many of the proteins identified had not been detected in previous studies of BAL fluid; thus, the use of LC-tandem MS with LTQ may provide new information regarding potentially important patterns of protein expression associated with lifelong smoking.

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