scholarly journals RNA‐seq analysis identifies novel gene signatures common to SHP knockout mice and human steatosis, fibrosis, NASH and cirrhosis

2013 ◽  
Vol 27 (S1) ◽  
Author(s):  
Rana Smalling ◽  
Don Delker ◽  
Yuxia Zhang ◽  
Michael McGuiness ◽  
Shuanghu Liu ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Rna Seq ◽  
Gene Signatures ◽  
Novel Gene

scholarly journals Angelman Syndrome and Angelman-like Syndromes Share the Same Calcium-Related Gene Signatures

2021 ◽  
Vol 22 (18) ◽  
pp. 9870
Author(s):  
Julia Panov ◽  
Hanoch Kaphzan
Keyword(s):  
Angelman Syndrome ◽  
Neurodevelopmental Disorders ◽  
Clinical Presentation ◽  
Rna Seq ◽  
Related Gene ◽  
Bioinformatics Analyses ◽  
Gene Signatures ◽  
Signature Genes ◽  
Gene Expression Analyses ◽  
Differential Gene

Angelman-like syndromes are a group of neurodevelopmental disorders that entail clinical presentation similar to Angelman Syndrome (AS). In our previous study, we showed that calcium signaling is disrupted in AS, and we identified calcium-target and calcium-regulating gene signatures that are able to differentiate between AS and their controls in different models. In the herein study, we evaluated these sets of calcium-target and calcium-regulating genes as signatures of AS-like and non-AS-like syndromes. We collected a number of RNA-seq datasets of various AS-like and non-AS-like syndromes and performed Principle Component Analysis (PCA) separately on the two sets of signature genes to visualize the distribution of samples on the PC1–PC2 plane. In addition to the evaluation of calcium signature genes, we performed differential gene expression analyses to identify calcium-related genes dysregulated in each of the studied syndromes. These analyses showed that the calcium-target and calcium-regulating signatures differentiate well between AS-like syndromes and their controls. However, in spite of the fact that many of the non-AS-like syndromes have multiple differentially expressed calcium-related genes, the calcium signatures were not efficient classifiers for non-AS-like neurodevelopmental disorders. These results show that features based on clinical presentation are reflected in signatures derived from bioinformatics analyses and suggest the use of bioinformatics as a tool for classification.

scholarly journals Characterization of Poldip2 knockout mice: avoiding incorrect gene targeting

2021 ◽  
Author(s):  
Bernard Lassègue ◽  
Sandeep Kumar ◽  
Rohan Mandavilli ◽  
Keke Wang ◽  
Michelle Tsai ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Cell Clone ◽  
Gene Trap ◽  
Rna Seq ◽  
Multifunctional Protein ◽  
Cellular Processes ◽  
Depth Study ◽  
Perinatal Lethality ◽  
Knockout Line

AbstractPOLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from two limitations: perinatal lethality in homozygotes and constitutive Poldip2 inactivation. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, an RNA-seq experiment was performed in constitutive knockout carotid arteries. Results support the involvement of POLDIP2 in multiple cellular processes and provide new opportunities for future in-depth study of its functions.

scholarly journals Identification of a novel gene fusion RNF213-SLC26A11 in chronic myeloid leukemia by RNA-Seq

2012 ◽  
Vol 7 (2) ◽  
pp. 591-597 ◽  
Author(s):  
JIAN-BO ZHOU ◽  
TING ZHANG ◽  
BEN-FANG WANG ◽  
HAI-ZHEN GAO ◽  
XIN XU
Keyword(s):  
Chronic Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Gene Fusion ◽  
Rna Seq ◽  
Novel Gene

Morphological classification of pancreatic ductal adenocarcinoma that predicts molecular subtypes and correlates with clinical outcome

Gut ◽  
2019 ◽  
Vol 69 (2) ◽  
pp. 317-328 ◽  
Author(s):  
Sangeetha N Kalimuthu ◽  
Gavin W Wilson ◽  
Robert C Grant ◽  
Matthew Seto ◽  
Grainne O’Kane ◽  
...  
Keyword(s):  
Pancreatic Ductal Adenocarcinoma ◽  
Molecular Subtypes ◽  
Differentially Expressed Gene ◽  
Biological Significance ◽  
Treatment Strategies ◽  
Ductal Adenocarcinoma ◽  
Rna Seq ◽  
Gene Signatures ◽  
Significant Difference ◽  
Morphological Patterns

IntroductionTranscriptional analyses have identified several distinct molecular subtypes in pancreatic ductal adenocarcinoma (PDAC) that have prognostic and potential therapeutic significance. However, to date, an indepth, clinicomorphological correlation of these molecular subtypes has not been performed. We sought to identify specific morphological patterns to compare with known molecular subtypes, interrogate their biological significance, and furthermore reappraise the current grading system in PDAC.DesignWe first assessed 86 primary, chemotherapy-naive PDAC resection specimens with matched RNA-Seq data for specific, reproducible morphological patterns. Differential expression was applied to the gene expression data using the morphological features. We next compared the differentially expressed gene signatures with previously published molecular subtypes. Overall survival (OS) was correlated with the morphological and molecular subtypes.ResultsWe identified four morphological patterns that segregated into two components (‘gland forming’ and ‘non-gland forming’) based on the presence/absence of well-formed glands. A morphological cut-off (≥40% ‘non-gland forming’) was established using RNA-Seq data, which identified two groups (A and B) with gene signatures that correlated with known molecular subtypes. There was a significant difference in OS between the groups. The morphological groups remained significantly prognostic within cancers that were moderately differentiated and classified as ‘classical’ using RNA-Seq.ConclusionOur study has demonstrated that PDACs can be morphologically classified into distinct and biologically relevant categories which predict known molecular subtypes. These results provide the basis for an improved taxonomy of PDAC, which may lend itself to future treatment strategies and the development of deep learning models.

scholarly journals Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease

2013 ◽  
Vol 305 (5) ◽  
pp. G364-G374 ◽  
Author(s):  
Rana L. Smalling ◽  
Don A. Delker ◽  
Yuxia Zhang ◽  
Natalia Nieto ◽  
Michael S. Mcguiness ◽  
...  
Keyword(s):  
Liver Disease ◽  
Hepatitis C ◽  
Liver Function ◽  
Chronic Liver Disease ◽  
Nuclear Receptor ◽  
Liver Diseases ◽  
Human Liver ◽  
Chronic Liver ◽  
Rna Seq ◽  
Gene Signatures

The molecular mechanisms behind human liver disease progression to cirrhosis remain elusive. Nuclear receptor small heterodimer partner (SHP/ Nr0b2) is a hepatic tumor suppressor and a critical regulator of liver function. SHP expression is diminished in human cirrhotic livers, suggesting a regulatory role in human liver diseases. The goal of this study was to identify novel SHP-regulated genes that are involved in the development and progression of chronic liver disease. To achieve this, we conducted the first comprehensive RNA sequencing (RNA-seq) analysis of Shp−/− mice, compared the results with human hepatitis C cirrhosis RNA-seq and nonalcoholic steatohepatitis (NASH) microarray datasets, and verified novel results in human liver biospecimens. This approach revealed new gene signatures associated with chronic liver disease and regulated by SHP. Several genes were selected for validation of physiological relevance based on their marked upregulation, novelty with regard to liver function, and involvement in gene pathways related to liver disease. These genes include peptidoglycan recognition protein 2, dual specific phosphatase-4, tetraspanin 4, thrombospondin 1, and SPARC-related modular calcium binding protein-2, which were validated by qPCR analysis of 126 human liver specimens, including steatosis, fibrosis, and NASH, alcohol and hepatitis C cirrhosis, and in mouse models of liver inflammation and injury. This RNA-seq analysis identifies new genes that are regulated by the nuclear receptor SHP and implicated in the molecular pathogenesis of human chronic liver diseases. The results provide valuable transcriptome information for characterizing mechanisms of these diseases.

scholarly journals Identification of novel gene signatures in patients with atopic dermatitis complicated by eczema herpeticum

2014 ◽  
Vol 134 (4) ◽  
pp. 848-855 ◽  
Author(s):  
Lianghua Bin ◽  
Michael G. Edwards ◽  
Ryan Heiser ◽  
Joanne E. Streib ◽  
Brittany Richers ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Gene Signatures ◽  
Eczema Herpeticum ◽  
Novel Gene

scholarly journals Zkscan3 affects erythroblast development by regulating the transcriptional activity of GATA1 and KLF1 in mice

2021 ◽  
Author(s):  
Zixuan Li ◽  
Binjie Sheng ◽  
Tingting Zhang ◽  
Tian Wang ◽  
Dan Chen ◽  
...  
Keyword(s):  
Significant Role ◽  
Knockout Mice ◽  
Transcriptional Activity ◽  
Early Stage ◽  
Quantitative Polymerase Chain Reaction ◽  
Tumor Development ◽  
Rna Seq ◽  
Mice Model ◽  
First Time

AbstractZKSCAN3 encodes a zinc-finger transcription factor that regulates the expression of important genes and plays a significant role in tumor development, pathogenesis, and metastasis. However, its biological functions under normal physiological conditions remain largely unknown. In our previous studies, using flow cytometry, we found that the deletion of Zkscan3 may cause abnormal erythropoiesis. In this study, we found that, in a Zkscan3 knockout mice model, the number of splenic early-stage (basophilic-erythroblasts) and late-stage (chromatophilic-erythroblasts to polychromatophilic-erythroblasts through orthochromatophilic-erythroblasts) erythroblasts increased, whereas the number of late erythroblasts in the bone marrow decreased. Moreover, the phenotype was exacerbated after treating mice with phenylhydrazine (PHZ), which causes severe hemolytic anemia. In the knockout mice treated with PHZ, the percentage of reticulocyte in the peripheral blood conspicuously increased, whereas MCHC and red blood cells decreased. Then, we performed RNA-seq and quantitative-polymerase chain reaction assay and found that the expression of GATA1 and Tiam1 in erythroblasts were upregulated, whereas KLF1 was downregulated. Luciferase assays showed that Zkscan3 inhibited the transcription of GATA1 and Tiam1 and promoted the expression of KLF1. Additionally, ChIP and CO-IP results confirmed that Zkscan3 directly interacts with GATA1 and inhibits its transcriptional activity in MEL cells. Our results demonstrate, for the first time, the significant role of Zkscan3 in physiological erythropoiesis through the interaction with GATA1, both at the DNA and protein level, and with Tiam1 and KLF1 at the DNA level.

scholarly journals Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0247261
Author(s):  
Bernard Lassègue ◽  
Sandeep Kumar ◽  
Rohan Mandavilli ◽  
Keke Wang ◽  
Michelle Tsai ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Cell Clone ◽  
Gene Trap ◽  
Rna Seq ◽  
Multifunctional Protein ◽  
Cellular Processes ◽  
Depth Study ◽  
Perinatal Lethality ◽  
Knockout Line

POLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from three limitations: perinatal lethality in homozygotes, constitutive Poldip2 inactivation and inadvertent downregulation of the adjacent Tmem199 gene. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, RNA-seq and RT-qPCR experiments were performed in constitutive knockout arteries. Results show that POLDIP2 inactivation affects multiple cellular processes and provide new opportunities for future in-depth study of its functions.

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