Cryo‐injury procedure‐induced cardiac regeneration shows unique gene expression profiles in the newt Pleurodeles waltl

2021 ◽  
Author(s):  
Hitoshi Uemasu ◽  
Hiromi Ikuta ◽  
Takeshi Igawa ◽  
Makoto Suzuki ◽  
Mitsuki Kyakuno ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cardiac Regeneration ◽  
Unique Gene ◽  
Pleurodeles Waltl

scholarly journals TGFβ-1 and Wnt-3a interact to induce unique gene expression profiles in murine embryonic palate mesenchymal cells

2011 ◽  
Vol 31 (2) ◽  
pp. 128-133 ◽  
Author(s):  
Dennis R. Warner ◽  
Partha Mukhopadhyay ◽  
Guy N. Brock ◽  
Vasyl Pihur ◽  
M. Michele Pisano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mesenchymal Cells ◽  
Unique Gene

Unique Gene Expression Profiles of AML Patients with CEBPA Mutations.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 745-745
Author(s):  
Bas J. Wouters ◽  
Claudia A. Erpelinck ◽  
Peter J. Valk ◽  
Roel G. Verhaak ◽  
Bob Löwenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dominant Negative ◽  
Differentially Expressed ◽  
Rank Test ◽  
Insertion Mutation ◽  
Wild Type ◽  
Unique Gene ◽  
Cebpa Mutations

Abstract The transcription factor CCAAT/enhancer binding protein alpha (C/EBPalpha) is critical for granulopoiesis. 5–10% of patients with acute myeloid leukemia (AML) carry mutations in the coding region of the CEBPA gene. In a gene expression profiling study of 285 de novo AML patients we previously identified sixteen distinct clusters of AML (Valk et al, N Engl J Med 2004). Eighteen patients (6.3%) carried mutations in CEBPA, and 17 of them were found in two clusters (clusters #4 and #15), indicating that patients with CEBPA mutations exhibit unique gene expression profiles. In cluster #15, all specimens (n=8) carried CEBPA mutations, whereas in cluster #4 CEBPA mutations were found in 9 out of 15 cases. The other 6 cases in this subgroup showed low or no CEBPA mRNA expression, and in 4 of the latter the gene appeared to be switched off by CpG-hypermethylation. We sought to understand why CEBPA mutations were found in two separate clusters, and asked whether we could identify differences between the two clusters. We found no difference when analyzing CEBPA mutation types as most specimens in both clusters carried both an N-terminal truncation and a C-terminal in-frame insertion mutation. Morphologically, specimens in cluster #4 appeared to be less differentiated as compared to patients in cluster #15 (predominant FAB-types being M1 and M2, respectively). With respect to overall survival, patients in cluster #15 tend to have a slightly worse prognosis than patients with mutations in cluster #4 (Kaplan-Meier method, log-rank test, p=0.03). Although two separate clusters were formed, we felt that genes present in expression profiles of both cluster #4 and #15 could be potentially interesting as they could be linked to defective C/EBPalpha functioning. Strikingly, out of the 22 genes differentially expressed in cluster #15, 12 were also differentially expressed in cluster #4, including CTNNA1, TUBB-5, NDFIP1, SFXN3, KIAA0746 and TENS1. Interestingly, all 12 genes were significantly downregulated, suggesting that they could be targets of wild type C/EBPalpha and/or downregulated by mutated C/EBPalpha. To test this hypothesis, we introduced either wild type or mutant CEBPA-ER into 32Dcl1, a cell line model constitutively expressing the human G-CSFR. In line with previous reports, we found that activation of C/EBPalpha by addition of beta-estradiol resulted in proliferation arrest and differentiation of these cells within two days, even in the presence of IL-3. Expression levels of the C/EBPalpha target gene CSF3R increased drastically (12-fold after 24 hours, 53-fold after 48 hours) upon stimulation with beta-estradiol as compared to unstimulated or empty vector control clones. Experiments with clones expressing a C-terminal mutant carrying an 18-nt insertion in the bZIP region showed that proliferation was only modestly inhibited and that differentiation was severely impaired both in the presence of IL-3 or G-CSF. Interestingly, no upregulation of the CSF3R gene was observed following beta-estradiol stimulation of mutant CEBPA-ER in the presence of IL-3. Moreover, activation of mutant C/EBPalpha counteracted the induction of CSF3R expression observed following G-CSF activation. These findings suggest that C-terminal C/EBPalpha mutants can have a dominant negative role in AML. Our studies demonstrate that 32Dcl1-CEBPA-ER cells provide a useful model to further elucidate the possible relationships of C/EBPalpha and C/EBPalpha mutants with differentially expressed genes identified in the gene expression studies.

scholarly journals Machine learning algorithms reveal unique gene expression profiles in muscle biopsies from patients with different types of myositis

2020 ◽  
Vol 79 (9) ◽  
pp. 1234-1242 ◽  
Author(s):  
Iago Pinal-Fernandez ◽  
Maria Casal-Dominguez ◽  
Assia Derfoul ◽  
Katherine Pak ◽  
Frederick W Miller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Learning Algorithm ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Machine Learning Algorithms ◽  
Recursive Feature Elimination ◽  
Machine Learning Algorithm ◽  
Unique Gene ◽  
Muscle Biopsies

ObjectivesMyositis is a heterogeneous family of diseases that includes dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotising myopathy (IMNM), inclusion body myositis (IBM), polymyositis and overlap myositis. Additional subtypes of myositis can be defined by the presence of myositis-specific autoantibodies (MSAs). The purpose of this study was to define unique gene expression profiles in muscle biopsies from patients with MSA-positive DM, AS and IMNM as well as IBM.MethodsRNA-seq was performed on muscle biopsies from 119 myositis patients with IBM or defined MSAs and 20 controls. Machine learning algorithms were trained on transcriptomic data and recursive feature elimination was used to determine which genes were most useful for classifying muscle biopsies into each type and MSA-defined subtype of myositis.ResultsThe support vector machine learning algorithm classified the muscle biopsies with >90% accuracy. Recursive feature elimination identified genes that are most useful to the machine learning algorithm and that are only overexpressed in one type of myositis. For example, CAMK1G (calcium/calmodulin-dependent protein kinase IG), EGR4 (early growth response protein 4) and CXCL8 (interleukin 8) are highly expressed in AS but not in DM or other types of myositis. Using the same computational approach, we also identified genes that are uniquely overexpressed in different MSA-defined subtypes. These included apolipoprotein A4 (APOA4), which is only expressed in anti-3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) myopathy, and MADCAM1 (mucosal vascular addressin cell adhesion molecule 1), which is only expressed in anti-Mi2-positive DM.ConclusionsUnique gene expression profiles in muscle biopsies from patients with MSA-defined subtypes of myositis and IBM suggest that different pathological mechanisms underly muscle damage in each of these diseases.

Histological Subtypes of Canine Lymphoma are Characterized by Unique Gene Expression Profiles

2005 ◽  
Vol 3 (1) ◽  
pp. 46-46
Author(s):  
W. C. Kisseberth ◽  
C. E. Kosarek ◽  
H. Auer ◽  
K. Kornacker ◽  
V. E. Valli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Histological Subtypes ◽  
Canine Lymphoma ◽  
Unique Gene

scholarly journals Anopheles aquasalis Infected by Plasmodium vivax Displays Unique Gene Expression Profiles when Compared to Other Malaria Vectors and Plasmodia

PLoS ONE ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. e9795 ◽  
Author(s):  
Ana C. Bahia ◽  
Marina S. Kubota ◽  
Antonio J. Tempone ◽  
Waleria D. Pinheiro ◽  
Wanderli P. Tadei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodium Vivax ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Malaria Vectors ◽  
Unique Gene ◽  
Anopheles Aquasalis
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