Microarray Analyses of Gene Expression during Chondrocyte Differentiation Identifies Novel Regulators of Hypertrophy

Ordered chondrocyte differentiation and maturation is required for normal skeletal development, but the intracellular pathways regulating this process remain largely unclear. We used Affymetrix microarrays to examine temporal gene expression patterns during chondrogenic differentiation in a mouse micromass culture system. Robust normalization of the data identified 3300 differentially expressed probe sets, which corresponds to 1772, 481, and 249 probe sets exhibiting minimum 2-, 5-, and 10-fold changes over the time period, respectively. GeneOntology annotations for molecular function show changes in the expression of molecules involved in transcriptional regulation and signal transduction among others. The expression of identified markers was confirmed by RT-PCR, and cluster analysis revealed groups of coexpressed transcripts. One gene that was up-regulated at later stages of chondrocyte differentiation was Rgs2. Overexpression of Rgs2 in the chondrogenic cell line ATDC5 resulted in accelerated hypertrophic differentiation, thus providing functional validation of microarray data. Collectively, these analyses provide novel information on the temporal expression of molecules regulating endochondral bone development.

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Prolyl Hydroxylase Domain-Containing Protein 3 Gene Expression in Chondrocytes Is Not Essential for Bone Development in Mice

Cells ◽

10.3390/cells10092200 ◽

2021 ◽

Vol 10 (9) ◽

pp. 2200

Author(s):

Weirong Xing ◽

Sheila Pourteymoor ◽

Gustavo A. Gomez ◽

Yian Chen ◽

Subburaman Mohan

Keyword(s):

Gene Expression ◽

Bone Formation ◽

Bone Mass ◽

Trabecular Bone ◽

Bone Volume ◽

Endochondral Bone Formation ◽

Chondrocyte Differentiation ◽

Trabecular Bone Volume ◽

Endochondral Bone ◽

Trabecular Bone Mass

We previously showed that conditional disruption of the Phd2 gene in chondrocytes led to a massive increase in long bone trabecular bone mass. Loss of Phd2 gene expression or inhibition of PHD2 activity by a specific inhibitor resulted in a several-fold compensatory increase in Phd3 expression in chondrocytes. To determine if expression of PHD3 plays a role in endochondral bone formation, we conditionally disrupted the Phd3 gene in chondrocytes by crossing Phd3 floxed (Phd3flox/flox) mice with Col2α1-Cre mice. Loss of Phd3 expression in the chondrocytes of Cre+; Phd3flox/flox conditional knockout (cKO) mice was confirmed by real time PCR. At 16 weeks of age, neither body weight nor body length was significantly different in the Phd3 cKO mice compared to Cre−; Phd3flox/flox wild-type (WT) mice. Areal BMD measurements of total body as well as femur, tibia, and lumbar skeletal sites were not significantly different between the cKO and WT mice at 16 weeks of age. Micro-CT measurements revealed significant gender differences in the trabecular bone volume adjusted for tissue volume at the secondary spongiosa of the femur and the tibia for both genotypes, but no genotype difference was found for any of the trabecular bone measurements of either the femur or the tibia. Trabecular bone volume of distal femur epiphysis was not different between cKO and WT mice. Histology analyses revealed Phd3 cKO mice exhibited a comparable chondrocyte differentiation and proliferation, as evidenced by no changes in cartilage thickness and area in the cKO mice as compared to WT littermates. Consistent with the in vivo data, lentiviral shRNA-mediated knockdown of Phd3 expression in chondrocytes did not affect the expression of markers of chondrocyte differentiation (Col2, Col10, Acan, Sox9). Our study found that Phd2 but not Phd3 expressed in chondrocytes regulates endochondral bone formation, and the compensatory increase in Phd3 expression in the chondrocytes of Phd2 cKO mice is not the cause for increased trabecular bone mass in Phd2 cKO mice.

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Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series

Journal of Integrative Bioinformatics ◽

10.1515/jib-2011-175 ◽

2011 ◽

Vol 8 (3) ◽

pp. 73-89 ◽

Cited By ~ 11

Author(s):

André V. Carreiro ◽

Orlando Anunciação ◽

João A. Carriço ◽

Sara C. Madeira

Keyword(s):

Gene Expression ◽

Time Series ◽

Expression Patterns ◽

Classification Problems ◽

Temporal Perspective ◽

Temporal Gene Expression ◽

Gene Expression Time Series ◽

Prognostic Prediction ◽

Multiple Sclerosis Patients ◽

Expression Time

Summary The constant drive towards a more personalized medicine led to an increasing interest in temporal gene expression analyzes. It is now broadly accepted that considering a temporal perspective represents a great advantage to better understand disease progression and treatment results at a molecular level. In this context, biclustering algorithms emerged as an important tool to discover local expression patterns in biomedical applications, and CCC-Biclustering arose as an efficient algorithm relying on the temporal nature of data to identify all maximal temporal patterns in gene expression time series. In this work, CCC-Biclustering was integrated in new biclustering-based classifiers for prognostic prediction. As case study we analyzed multiple gene expression time series in order to classify the response of Multiple Sclerosis patients to the standard treatment with Interferon-β, to which nearly half of the patients reveal a negative response. In this scenario, using an effective predictive model of a patient’s response would avoid useless and possibly harmful therapies for the non-responder group. The results revealed interesting potentialities to be further explored in classification problems involving other (clinical) time series.

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The trabecula culture system: a novel technique to study contractile parameters over a multiday time period

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.1998.274.5.h1481 ◽

1998 ◽

Vol 274 (5) ◽

pp. H1481-H1488 ◽

Cited By ~ 20

Author(s):

P. M. L. Janssen ◽

S. E. Lehnart ◽

J. Prestle ◽

J. C. Lynker ◽

P. Salfeld ◽

...

Keyword(s):

Gene Expression ◽

Protein Expression ◽

Contractile Function ◽

Expression Patterns ◽

Leucine Incorporation ◽

System A ◽

Time Period ◽

Incorporation Assay ◽

Force Time ◽

Ventricular Trabeculae

In the intact heart, various triggers induce alterations in gene expression that impact on contractile function. Because changes in gene expression reflect altered protein expression patterns after 12–48 h, we developed a system in which intact twitching cardiac trabeculae can be studied for multiday periods. Right ventricular trabeculae from pentobarbital sodium-anesthetized rabbits were mounted in a sterile, closed muscle chamber. Over the first 48 h, developed force (Fdev) did not significantly change: 102.3 and 98.9% of the initial Fdev was observed after 24 and 48 h, respectively ( n = 8). Also, neither diastolic force, time from peak to 50% relaxation (RT50), nor protein synthesis measured by a [3H]leucine incorporation assay changed significantly over time. Contractile response after >48 h to an increase in extracellular calcium concentration (1.8 to 2.5 mM; Fdevincreased 43.5%, n = 2) or to 1 μM isoproterenol (Fdevincreased 138.6% and RT50decreased 34.9%, n = 2) was similar to those observed in freshly dissected preparations. In conclusion, this system can investigate contractile function of multicellular preparations under well-defined physiological conditions after events that alter gene and consequent protein expression.

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Optic nerve crush induces spatial and temporal gene expression patterns in retina and optic nerve of BALB/cJ mice

Molecular Neurodegeneration ◽

10.1186/1750-1326-9-14 ◽

2014 ◽

Vol 9 (1) ◽

pp. 14 ◽

Cited By ~ 10

Author(s):

Tasneem P Sharma ◽

Colleen M McDowell ◽

Yang Liu ◽

Alex H Wagner ◽

David Thole ◽

...

Keyword(s):

Gene Expression ◽

Optic Nerve ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Optic Nerve Crush ◽

Nerve Crush ◽

Temporal Gene Expression

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Comprehensive regional and temporal gene expression profiling of the rat brain during the first 24 h after experimental stroke identifies dynamic ischemia-induced gene expression patterns, and reveals a biphasic activation of genes in surviving tissue

Journal of Neurochemistry ◽

10.1111/j.1471-4159.2005.03508.x ◽

2006 ◽

Vol 96 (1) ◽

pp. 14-29 ◽

Cited By ~ 60

Author(s):

Mattias Rickhag ◽

Tadeusz Wieloch ◽

Gunilla Gido ◽

Eskil Elmer ◽

Morten Krogh ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Rat Brain ◽

Expression Profiling ◽

Expression Patterns ◽

Experimental Stroke ◽

Gene Expression Patterns ◽

Temporal Gene Expression

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Dissecting the contributions of time and microbe density to variation in immune gene expression

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2017.0727 ◽

2017 ◽

Vol 284 (1859) ◽

pp. 20170727 ◽

Cited By ~ 11

Author(s):

Ann T. Tate ◽

Andrea L. Graham

Keyword(s):

Gene Expression ◽

Functional Outcomes ◽

Expression Patterns ◽

Immune Gene ◽

Cross Sectional ◽

Underlying Assumption ◽

Temporal Gene Expression ◽

Immune Gene Expression ◽

Highly Correlated ◽

Almost All

Widespread differential expression of immunological genes is a hallmark of the response to infection in almost all surveyed taxa. However, several challenges remain in the attempt to connect differences in gene expression with functional outcomes like parasite killing and host survival. For example, temporal gene expression patterns are not always monotonic (unidirectional slope), yielding results that qualitatively depend on the time point selected for analysis. They may also be correlated to microbe density, confounding the strength of an immune response and resistance to parasites. In this study, we analyse these relationships in an mRNA-seq time series of Tribolium castaneum infected with Bacillus thuringiensis . Our results suggest that many extracellular immunological components with known roles in immunity, like antimicrobial peptides and recognition proteins, are highly correlated to microbe load. On the other hand, intracellular components of immunological signalling pathways overwhelmingly show non-monotonic temporal patterns of gene expression, despite the underlying assumption of monotonicity in most ecological and comparative transcriptomics studies that rely on cross-sectional analyses. Our results raise a host of new questions, including to what extent variation in host resistance, infection tolerance and immunopathology can be explained by variation in the slope or sensitivity of these newly characterized patterns.

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H3K36 methyltransferase NSD1 regulates chondrocyte differentiation for skeletal development and fracture repair

Bone Research ◽

10.1038/s41413-021-00148-y ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Rui Shao ◽

Zhong Zhang ◽

Zhan Xu ◽

Huiling Ouyang ◽

Lijun Wang ◽

...

Keyword(s):

Epigenetic Regulation ◽

Chondrogenic Differentiation ◽

Transcriptional Control ◽

Bone Development ◽

Skeletal Development ◽

Hypoxia Inducible Factor ◽

Fracture Repair ◽

Skeletal Growth ◽

Long Bone ◽

Chondrocyte Differentiation

AbstractChondrocyte differentiation is a critical process for endochondral ossification, which is responsible for long bone development and fracture repair. Considerable progress has been made in understanding the transcriptional control of chondrocyte differentiation; however, epigenetic regulation of chondrocyte differentiation remains to be further studied. NSD1 is a H3K36 (histone H3 at lysine 36) methyltransferase. Here, we showed that mice with Nsd1 deficiency in Prx1+ mesenchymal progenitors but not in Col2+ chondrocytes showed impaired skeletal growth and fracture healing accompanied by decreased chondrogenic differentiation. Via combined RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we identified sex determining region Y box 9 (Sox9), the key transcription factor of chondrogenic differentiation, as a functional target gene of NSD1. Mechanistically, NSD1 regulates Sox9 expression by modulating H3K36me1 and H3K36me2 levels in the Sox9 promoter region, constituting a novel epigenetic regulatory mechanism of chondrogenesis. Moreover, we found that NSD1 can directly activate the expression of hypoxia-inducible factor 1α (HIF1α), which plays a vital role in chondrogenic differentiation through its regulation of Sox9 expression. Collectively, the results of our study reveal crucial roles of NSD1 in regulating chondrogenic differentiation, skeletal growth, and fracture repair and expand our understanding of the function of epigenetic regulation in chondrogenesis and skeletal biology.

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Pseudo-Location: A novel predictor for predicting pseudo-temporal gene expression patterns using spatial functional regression

10.1101/2020.06.11.145565 ◽

2020 ◽

Author(s):

Kyungmin Ahn ◽

Hironobu Fujiwara

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Functional Regression ◽

Rna Seq ◽

Temporal Gene Expression ◽

Early Stages ◽

The Future

Statement of withdrawalThe authors have withdrawn version 1 of this manuscript because a draft manuscript, which was still in the early stages of preparation and required major revisions including the replacement of the source RNA-seq datasets, was erroneously submitted. The authors do not wish this version to be cited as reference for this study. We will post a revised manuscript in the future. If you have any questions, please contact the corresponding author.

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