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| Status |
Public on Nov 19, 2019 |
| Title |
Tissue specific human fibroblast differential expression based on RNAsequencing analysis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background:Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence geneexpression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumedadaptation upon various mechanical loads. The purpose of this study was to compare the vocal fold fibroblastgenotype, known for its unique mechanically stressful tissue environment, with cellular counterparts at various otheranatomic locales to identify differences in functional gene expression profiles.
Results:By using RNA-seq technology, we identified differentially expressed gene programs (DEseq2) among sevennormal human fibroblast primary cell lines from healthy cadavers, which included: vocal fold, trachea, lung, abdomen,scalp, upper gingiva, and soft palate. Unsupervised gene expression analysis yielded 6216 genes differentially expressedacross all anatomic sites. Hierarchical cluster analysis revealed grouping based on anatomic site origin rather thandonor, suggesting global fibroblast phenotype heterogeneity. Sex and age-related effects were negligible. Functionalenrichment analyses based on separate post-hoc 2-group comparisons revealed several functional themes within thevocal fold fibroblast related to transcription factors for signaling pathways regulating pluripotency of stem cells andextracellular matrix components such as cell signaling, migration, proliferation, and differentiation potential.
Conclusions:Human fibroblasts display a phenomenon of global topographic differentiation, which is maintained inisolation via in vitro assays. Epigenetic mechanical influences on vocal fold tissue may play a role in uniquely modellingand maintaining the local environmental cellular niche during homeostasis with vocal fold fibroblasts distinctlyspecialized related to their anatomic positional and developmental origins established during embryogenesis.
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| Overall design |
Comppared mRNA profiles of a total of 34 samples from 7 different locations controlling for age and sex effect.
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| Contributor(s) |
Foote AG, Thibeault SL, Kendziorski C, Wang Z |
| Citation(s) |
31014251 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DC004336 |
Engineering the Vocal Fold Extracellular Matrix |
UNIVERSITY OF WISCONSIN MADISON |
Susan Thibeault |
| T32 DC009401 |
University of Wisconsin Voice Research Training Program (T32) |
UNIVERSITY OF WISCONSIN MADISON |
Susan Thibeault |
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| Submission date |
Nov 18, 2019 |
| Last update date |
Nov 23, 2019 |
| Contact name |
Ziyue Wang |
| E-mail(s) |
zwang667@wisc.edu
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| Organization name |
UW Madison
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| Street address |
425 Henry Mall
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (34)
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| Relations |
| BioProject |
PRJNA590132 |
| SRA |
SRP230383 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140523_Normalized_Matrix.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE140523_RAW.tar |
3.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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