ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels

2005 ◽  
Vol 111 (1) ◽  
pp. 79-87 ◽  
Author(s):  
P. Savolainen ◽  
C. Fitzsimmons ◽  
L. Arvestad ◽  
L. Andersson ◽  
J. Lundeberg
Keyword(s):  
White Leghorn ◽  
Expression Levels ◽  
Red Junglefowl

New microRNA-based diagnostic test for lung cancer classification.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10528-10528
Author(s):  
Ranit Aharonov ◽  
Gila Lithwick Yanai ◽  
Hila Benjamin ◽  
Mats Olot Sanden ◽  
Marluce Bibbo ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cell Carcinoma ◽  
Expression Profiles ◽  
Lung Tumors ◽  
Small Cell ◽  
Diagnostic Methods ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Cancer Types

10528 Background: Lung cancer is the leading cause of cancer deaths in the US. Treatment options are determined by tumor subtyping, for which there is lack of standardized, objective, and highly accurate techniques. In 20%-30% of cases significant limitations of tumor quantity and quality prevent full classification of the tumor using traditional diagnostic methods. Using microRNA microarray data generated from over a hundred formalin-fixed, paraffin-embedded (FFPE) primary lung cancer samples, we have identified microRNA expression profiles that differ significantly for the main lung cancer types. Based on these findings, we have developed and validated a microRNA-based qRT-PCR assay that differentiates primary lung cancers into four types: squamous cell carcinoma, non-squamous non-small cell lung cancer, carcinoid and small cell carcinoma. Methods: Over 700 primary tumor samples from different histological types of lung cancer were collected. Samples included FFPE blocks from resection or biopsies and cell blocks from cytology specimens including fine needle aspiration, bronchial brushing and bronchial washing. High-quality RNA was extracted from the samples using proprietary protocols. Expression levels of potential microRNA biomarkers were profiled using microarrays followed by a sensitive and specific qRT-PCR platform. An assay for lung tumors classification using 8 microRNAs on qRT-PCR was developed based on data from 261 samples. This assay was validated on an independent blinded set of 451 cytological and pathological samples. Results: Using the expression levels of 8 microRNAs measured in qRT-PCR, accurate classification of the primary lung tumors into the four main cancer types is obtained. The microRNA-based assay reached an accuracy of 94%. Moreover, cytological samples composed over 50% of the validation set and reached an accuracy of 95%. Conclusions: We present here a new microRNA-based assay for the classification of the four main types of lung cancer based only on the expression of 8 microRNAs. This assay displays very high levels of accuracy for both pathological and cytological samples. The assay comprises a standardized, well-tested and objective tool which can assist physicians in the diagnosis of lung cancer.

Integrated multi-omic analysis to reveal comprehensive tumor heterogeneity and novel immunophenotypic classification in primary liver cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15662-e15662
Author(s):  
Qi Zhang ◽  
Yu Lou ◽  
Xueli Bai ◽  
Tingbo Liang
Keyword(s):  
Tumor Heterogeneity ◽  
Single Cell Analysis ◽  
Primary Liver Cancer ◽  
Treatment Strategies ◽  
Local Immunity ◽  
Expression Levels ◽  
Chain Reactions ◽  
Prognostic Prediction ◽  
Practice Methods

e15662 Background: Hepatocellular carcinoma (HCC) is heterogeneous,especially in multifocal tumors, which decreases the efficacy of clinical treatments. Understanding tumor heterogeneity is critical when developingnovel treatment strategies. However, a comprehensive investigation of tumor heterogeneity in HCC is lacking, and the available evidence regarding tumor heterogeneity has not ledto improvements inclinical practice. Methods: We harvested 42 samples from eight HCC patients and evaluatedtumor heterogeneity using whole-exome sequencing, RNA sequencing, mass spectrometry-based proteomics and metabolomics, cytometry by time-of-flight, and single-cell analysis. Immunohistochemistry and quantitative polymerase chain reactions (qPCRs) were performed to confirm the expression levels of genes. Results: Tumor heterogeneity is considerable with regard to the genomes, transcriptomes, proteomes, and metabolomes of lesions and tumors. The immune status oftheHCC microenvironment had a relatively low level of heterogeneity. Targeting local immunity could be a suitable intervention with balanced precision and practicability. By clustering immune cells in the HCC microenvironment, we identified three distinctive HCC subtypes with immunocompetent, immunodeficient, and immunosuppressive features. We further revealed the specific metabolic features and cytokine/chemokine expression levels of the different subtypes. Determiningthe expression levels of PTPRCand FOXP3using qPCR and immunohistochemistry in two independent HCC cohorts facilitated the correct classification of HCC patients and the prediction of their prognosis. Conclusions: There is comprehensive intratumoral and intertumoral heterogeneity inall dimensions ofHCC. Based on the results, we propose a novel immunophenotypic classification of HCCs that facilitates prognostic prediction and may support decision making with regard to the choice of therapy.

Fearfulness in red junglefowl and domesticated White Leghorn chickens

2009 ◽  
Vol 81 (1) ◽  
pp. 39-43 ◽  
Author(s):  
Magnus Campler ◽  
Markus Jöngren ◽  
Per Jensen
Keyword(s):  
White Leghorn ◽  
Red Junglefowl

Major Growth QTLs in Fowl Are Related to Fearful Behavior: Possible Genetic Links Between Fear Responses and Production Traits in a Red Junglefowl × White Leghorn Intercross

2004 ◽  
Vol 34 (1) ◽  
pp. 121-130 ◽  
Author(s):  
Karin E. Schütz ◽  
Susanne Kerje ◽  
Lina Jacobsson ◽  
Björn Forkman ◽  
Örjan Carlborg ◽  
...  
Keyword(s):  
Production Traits ◽  
White Leghorn ◽  
Red Junglefowl

Gene expression diversity among Mycobacterium tuberculosis clinical isolates

Microbiology ◽  
2005 ◽  
Vol 151 (1) ◽  
pp. 5-14 ◽  
Author(s):  
Qian Gao ◽  
Katharine E. Kripke ◽  
Alok J. Saldanha ◽  
Weihong Yan ◽  
Susan Holmes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
T Cell ◽  
Drug Targets ◽  
Expression Patterns ◽  
Clinical Isolates ◽  
Expression Levels ◽  
Expression Variability ◽  
T Cell Antigens

Intraspecies genetic diversity has been demonstrated to be important in the pathogenesis and epidemiology of several pathogens, such as HIV, influenza, Helicobacter and Salmonella. It is also important to consider strain-to-strain variation when identifying drug targets and vaccine antigens and developing tools for molecular diagnostics. Here, the authors present a description of the variability in gene expression patterns among ten clinical isolates of Mycobacterium tuberculosis, plus the laboratory strains H37Rv and H37Ra, growing in liquid culture. They identified 527 genes (15 % of those tested) that are variably expressed among the isolates studied. The remaining genes were divided into three categories based on their expression levels: unexpressed (38 %), low to undetectable expression (31 %) and consistently expressed (16 %). The expression categories were compared with functional categories and three biologically interesting gene lists: genes that are deleted among clinical isolates, T-cell antigens and essential genes. There were significant associations between expression variability and the classification of genes as T-cell antigens, involved in lipid metabolism, PE/PPE, insertion sequences and phages, and deleted among clinical isolates. This survey of mRNA expression among clinical isolates of M. tuberculosis demonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions.

scholarly journals A new pathological classification of intrahepatic cholangiocarcinoma according to protein expression of SSTR2 and Bcl2

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Shoko Yamashita ◽  
Yuji Morine ◽  
Satoru Imura ◽  
Tetsuya Ikemoto ◽  
Yu Saito ◽  
...  
Keyword(s):  
Protein Expression ◽  
Intrahepatic Cholangiocarcinoma ◽  
Clinical Stage ◽  
Expression Patterns ◽  
Somatostatin Receptor ◽  
Survival Rates ◽  
Cell Leukemia ◽  
Expression Levels ◽  
B Cell Leukemia

Abstract Background No universal classification method for intrahepatic cholangiocarcinoma (IHCC) has been reported based on the embryological origin of biliary epithelial cells. The aim of this study was to classify IHCC according to protein expression levels of somatostatin receptor 2 (SSTR2) and b-cell leukemia/lymphoma 2 (Bcl2) and to elucidate the clinicopathological features of each group. Methods Fifty-two IHCC patients who underwent hepatic resection were enrolled in this study. Protein expression levels of SSTR2 and Bcl2 were examined using immunohistochemistry. Clinicopathological factors were compared between the three groups and prognostic factors were investigated. Results The patients were divided into three groups: SSTR2 positive and Bcl2 negative (p-Group H, n = 21), SSTR2 negative and Bcl2 positive (p-Group P, n = 14), and the indeterminate group (p-Group U, n = 17) for cases where SSTR2 and Bcl2 were both positive or both negative. All p-Group P cases displayed curability A or B. The 5-year survival rates of p-Group H and U patients were worse than those in p-Group P. p-Group H had higher T-factor, clinical stage, and incidence of periductal infiltration than p-Group P. Conclusions This method could be used to classify IHCC into peripheral and perihilar type by embryological expression patterns of SSTR2 and Bcl2.

The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs

2003 ◽  
Vol 34 (4) ◽  
pp. 264-274 ◽  
Author(s):  
S. Kerje ◽  
Ö. Carlborg ◽  
L. Jacobsson ◽  
K. Schütz ◽  
C. Hartmann ◽  
...  
Keyword(s):  
Adult Size ◽  
White Leghorn ◽  
Red Junglefowl
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