Comparison of murine gene expression profiles between spontaneous and radiation-induced myelogenous leukemias: Stochastic and probabilistic expression variances in the former vs radiation-specific expression commonalities in the latter

2009 ◽  
Vol 37 (2) ◽  
pp. 195-205.e19 ◽  
Author(s):  
Yoko Hirabayashi ◽  
Isao Tsuboi ◽  
Kunio Kitada ◽  
Katsuhide Igarashi ◽  
Yukio Kodama ◽  
...  
2017 ◽  
Vol 10 (4) ◽  
pp. 425-437 ◽  
Author(s):  
Isabel L. Jackson ◽  
Fitsum Baye ◽  
Chirayu P. Goswami ◽  
Barry P. Katz ◽  
Andrew Zodda ◽  
...  

2011 ◽  
Vol 23 (4) ◽  
pp. 282-288 ◽  
Author(s):  
C. Maenhaut ◽  
V. Detours ◽  
G. Dom ◽  
D. Handkiewicz-Junak ◽  
M. Oczko-Wojciechowska ◽  
...  

2005 ◽  
Vol 21 (3) ◽  
pp. 314-323 ◽  
Author(s):  
Henk P. J. Buermans ◽  
Everaldo M. Redout ◽  
Anja E. Schiel ◽  
René J. P. Musters ◽  
Marian Zuidwijk ◽  
...  

Myocardial right ventricular (RV) hypertrophy due to pulmonary hypertension is aimed at normalizing ventricular wall stress. Depending on the degree of pressure overload, RV hypertrophy may progress to a state of impaired contractile function and heart failure, but this cannot be discerned during the early stages of ventricular remodeling. We tested whether critical differences in gene expression profiles exist between ventricles before the ultimate development of either a compensated or decompensated hypertrophic phenotype. Both phenotypes were selectively induced in Wistar rats by a single subcutaneous injection of either a low or a high dose of the pyrrolizidine alkaloid monocrotaline (MCT). Spotted oligonucleotide microarrays were used to investigate pressure-dependent cardiac gene expression profiles at 2 wk after the MCT injections, between control rats and rats that would ultimately develop either compensated or decompensated hypertrophy. Clustering of significantly regulated genes revealed specific expression profiles for each group, although the degree of hypertrophy was still similar in both. The ventricles destined to progress to failure showed activation of pro-apoptotic pathways, particularly related to mitochondria, whereas the group developing compensated hypertrophy showed blocked pro-death effector signaling via p38-MAPK, through upregulation of MAPK phosphatase-1. In summary, we show that, already at an early time point, pivotal differences in gene expression exist between ventricles that will ultimately develop either a compensated or a decompensated phenotype, depending on the degree of pressure overload. These data reveal genes that may provide markers for the early prediction of clinical outcome as well as potential targets for early intervention.


2019 ◽  
Author(s):  
Billy Zeng ◽  
Benjamin S. Glicksberg ◽  
Patrick Newbury ◽  
Jing Xing ◽  
Ke Liu ◽  
...  

AbstractOne approach to precision medicine is to discover drugs that target molecularly defined diseases. Voluminous cancer patient gene expression profiles have been accumulated in public databases, enabling the creation of a cancer-specific expression signature. By matching this signature to perturbagen-induced gene expression profiles from large drug libraries, researchers can prioritize small molecules that present high potency to reverse expression of signature genes for further experimental testing of their efficacy. This approach has proven to be an efficient and cost-effective way to identify efficacious drug candidates. However, the success of this approach requires multiscale procedures, imposing significant challenges to many labs. Therefore, we present OCTAD: an open workplace for virtually screening compounds targeting precise cancer patient groups using gene expression features. We release OCTAD as a web portal and standalone R workflow to allow experimental and computational scientists to easily navigate the tool. In this work, we describe this tool and demonstrate its potential for precision medicine.


2015 ◽  
Vol 124 (1_suppl) ◽  
pp. 6S-48S ◽  
Author(s):  
Shin-ya Nishio ◽  
Mitsuru Hattori ◽  
Hideaki Moteki ◽  
Keita Tsukada ◽  
Maiko Miyagawa ◽  
...  

Objectives:We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss.Methods:Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords.Results:Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans.Conclusions:The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.


Aging ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 2378-2387 ◽  
Author(s):  
Alexander M. Aliper ◽  
Marine E. Bozdaganyan ◽  
Philipp S. Orekhov ◽  
Alex Zhavoronkov ◽  
Andreyan N. Osipov

2019 ◽  
Vol 317 (1) ◽  
pp. L49-L56 ◽  
Author(s):  
Laurie C. Eldredge ◽  
Rane S. Creasy ◽  
Scott Presnell ◽  
Jason S. Debley ◽  
Sandra E. Juul ◽  
...  

Bronchopulmonary dysplasia (BPD) remains a devastating consequence of prematurity. Repeated inflammatory insults worsen lung injury, but there are no predictors for BPD-related respiratory outcomes or targeted therapies. We sought to understand inflammatory mechanisms in evolving BPD through molecular characterization of monocytes in tracheal aspirates from infants at risk for developing BPD. We performed flow cytometry targeting myeloid cell populations on prospectively collected tracheal aspirates from intubated patients born before 29 wk of gestation and <30 days old. We identified CD14+CD16+ (double-positive) and CD14+CD16− (single-positive) monocytes and characterized their gene expression profiles by RNA sequencing and quantitative PCR. We further analyzed differential gene expression between time points to evaluate changes in monocyte function over the first weeks of life. Expression of IL-1A, IL-1B, and IL-1 receptor antagonist mRNA was increased in monocytes collected at day of life ( DOL) 7, DOL 14, and DOL 28 compared with those collected at DOL 3. This study suggests that early changes in monocyte-specific IL-1 cytokine pathways may be associated with evolving BPD.


2010 ◽  
Vol 76 (16) ◽  
pp. 5533-5540 ◽  
Author(s):  
Carien C. G. M. Booijink ◽  
Jos Boekhorst ◽  
Erwin G. Zoetendal ◽  
Hauke Smidt ◽  
Michiel Kleerebezem ◽  
...  

ABSTRACT The human gastrointestinal (GI) tract provides home to a complex microbial community, collectively termed microbiota. Although major efforts have been made to describe the diversity and stability of the microbiota, functional studies have been largely restricted to intestinal isolates and include few community studies. The aim of this study was to explore the in situ gene expression of the fecal microbiota and to evaluate the RNA fingerprinting method cDNA-AFLP (cDNA amplified fragment length polymorphism) for this purpose. To this end, cDNA-AFLP analysis of enriched mRNA revealed that two healthy subjects showed highly divergent expression profiles with considerable fluctuations in time. Subsequent excision and sequence determination of bands from the mRNA-enriched profiles resulted in 122 identifiable sequences (transcripts and rRNAs). The classification of retrieved transcripts into functional clusters based on COG (cluster of orthologous genes) annotation showed that most assigned transcripts belonged to the metabolism cluster (26% of all sequences), underlining that even at the very end of the intestinal tract the microbiota is still very active. This study furthermore revealed that cDNA-AFLP is a useful tool to compare gene expression profiles in time in complex microbial communities.


2010 ◽  
Vol 143 (4) ◽  
pp. 525-530 ◽  
Author(s):  
Judy W. Lee ◽  
Richard A. Zoumalan ◽  
Cristian D. Valenzuela ◽  
Phuong D. Nguyen ◽  
John P. Tutela ◽  
...  

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