The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Diversity, topographic differentiation, and positional memory in human fibroblasts
Open accessAbstract
A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and organs, but the roles played by specific stromal cells in controlling the design and function of tissues remain poorly understood. The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. We characterized genome-wide patterns of gene expression in cultured fetal and adult human fibroblasts derived from skin at different anatomical sites. Fibroblasts from each site displayed distinct and characteristic transcriptional patterns, suggesting that fibroblasts at different locations in the body should be considered distinct differentiated cell types. Notable groups of differentially expressed genes included some implicated in extracellular matrix synthesis, lipid metabolism, and cell signaling pathways that control proliferation, cell migration, and fate determination. Several genes implicated in genetic diseases were found to be expressed in fibroblasts in an anatomic pattern that paralleled the phenotypic defects. Finally, adult fibroblasts maintained key features of HOX gene expression patterns established during embryogenesis, suggesting that HOX genes may direct topographic differentiation and underlie the detailed positional memory in fibroblasts.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Self-citationFinding Groups in Data: An Introduction to Cluster Analysis
Kaufman, L., & Rousseeuw, P. J. (1990) · Wiley Series in Probability and Statistics · doi:10.1002/9780470316801 · Cited by 7,344
SREBPs: activators of the complete program of cholesterol and fatty acid synthesis in the liver
Horton, J. D., Goldstein, J. L., & Brown, M. S. (2002) · Journal of Clinical Investigation · doi:10.1172/jci0215593 · Cited by 4,092
Cited by
Kalluri, R., & Zeisberg, M. (2006) · Nature Reviews Cancer · doi:10.1038/nrc1877 · Cited by 4,538
The biology and function of fibroblasts in cancer
Kalluri, R. (2016) · Nature Reviews Cancer · doi:10.1038/nrc.2016.73 · Cited by 4,366
Biomarkers for epithelial-mesenchymal transitions
Zeisberg, M., & Neilson, E. G. (2009) · Journal of Clinical Investigation · doi:10.1172/jci36183 · Cited by 2,299
Fibroblasts in fibrosis: novel roles and mediators
Kendall, R. T., & Feghali-Bostwick, C. A. (2014) · Frontiers in Pharmacology · doi:10.3389/fphar.2014.00123 · Cited by 1,082
Coexpression Analysis of Human Genes Across Many Microarray Data Sets
Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., & Pavlidis, P. (2004) · Genome Research · doi:10.1101/gr.1910904 · Cited by 770
Cancer associated fibroblasts (CAFs) in tumor microenvironment
Xing, F. (2010) · Frontiers in Bioscience · doi:10.2741/3613 · Cited by 682
Covas, D. T., Panepucci, R. A., Fontes, A. M., Silva, W. A., Orellana, M. D., Freitas, M. C. C., Neder, L., Santos, A. R. D., Peres, L. C., Jamur, M. C., et al. (2008) · Experimental Hematology · doi:10.1016/j.exphem.2007.12.015 · Cited by 610
The origin of fibroblasts and mechanism of cardiac fibrosis
Krenning, G., Zeisberg, E. M., & Kalluri, R. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22322 · Cited by 601
Fibroblast heterogeneity: more than skin deep
Sorrell, J. M., & Caplan, A. I. (2004) · Journal of Cell Science · doi:10.1242/jcs.01005 · Cited by 553
Karagiannis, G. S., Poutahidis, T., Erdman, S. E., Kirsch, R., Riddell, R. H., & Diamandis, E. P. (2012) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-12-0307 · Cited by 507
Motif module map reveals enforcement of aging by continual NF-κB activity
Adler, A. S., Sinha, S., Kawahara, T. L. A., Zhang, J. Y., Segal, E., & Chang, H. Y. (2007) · Genes & Development · doi:10.1101/gad.1588507 · Cited by 466
Self-citationWagner, J. R., Busche, S., Ge, B., Kwan, T., Pastinen, T., & Blanchette, M. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r37 · Cited by 446
Pilling, D., Fan, T., Huang, D., Kaul, B., & Gomer, R. H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007475 · Cited by 433
Cellular dynamics in the muscle satellite cell niche
Bentzinger, C. F., Wang, Y. X., Dumont, N. A., & Rudnicki, M. A. (2013) · The EMBO Reports · doi:10.1038/embor.2013.182 · Cited by 398
TGF-β Signaling in Cellular Senescence and Aging-Related Pathology
Tominaga, K., & Suzuki, H. I. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20205002 · Cited by 393
Intradermal adipocytes mediate fibroblast recruitment during skin wound healing
Schmidt, B. A., & Horsley, V. (2013) · Development · doi:10.1242/dev.087593 · Cited by 318
Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells
Murray, J. I., Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., & Botstein, D. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-11-0799 · Cited by 300
Self-citationA stromal address code defined by fibroblasts
Parsonage, G., Filer, A. D., Haworth, O., Nash, G. B., Rainger, G. E., Salmon, M., & Buckley, C. D. (2005) · Trends in Immunology · doi:10.1016/j.it.2004.11.014 · Cited by 297
Kung, H.-N., Marks, J. R., & Chi, J.-T. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002229 · Cited by 277
Self-citationNanoparticles for modulating tumor microenvironment to improve drug delivery and tumor therapy
Yang, S., & Gao, H. (2017) · Pharmacological Research · doi:10.1016/j.phrs.2017.05.004 · Cited by 256
Tumor-associated fibroblasts predominantly come from local and not circulating precursors
Arina, A., Idel, C., Hyjek, E. M., Alegre, M.-L., Wang, Y., Bindokas, V. P., Weichselbaum, R. R., & Schreiber, H. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600363113 · Cited by 238
The Role of Myofibroblasts in Physiological and Pathological Tissue Repair
Schuster, R., Younesi, F., Ezzo, M., & Hinz, B. (2023) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a041231 · Cited by 232
Elkabets, M., Gifford, A. M., Scheel, C., Nilsson, B., Reinhardt, F., Bray, M.-A., Carpenter, A. E., Jirström, K., Magnusson, K., Ebert, B. L., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci43757 · Cited by 201
Scleroderma pathogenesis: a pivotal role for fibroblasts as effector cells
Gilbane, A. J., Denton, C. P., & Holmes, A. M. (2013) · Arthritis Research & Therapy · doi:10.1186/ar4230 · Cited by 196
Nowarski, R., Jackson, R., & Flavell, R. A. (2017) · Cell · doi:10.1016/j.cell.2016.11.040 · Cited by 191
β-catenin signaling: a novel mediator of fibrosis and potential therapeutic target
Lam, A. P., & Gottardi, C. J. (2011) · Current Opinion in Rheumatology · doi:10.1097/bor.0b013e32834b3309 · Cited by 191
Cai, J., Tang, H., Xu, L., Wang, X., Yang, C., Ruan, S., Guo, J., Hu, S., & Wang, Z. (2012) · Carcinogenesis · doi:10.1093/carcin/bgr230 · Cited by 173
Muscle memory and a new cellular model for muscle atrophy and hypertrophy
Gundersen, K. (2016) · Journal of Experimental Biology · doi:10.1242/jeb.124495 · Cited by 169
Kasperkovitz, P. V., Timmer, T. C. G., Smeets, T. J., Verbeet, N. L., Tak, P. P., van baarsen, L. G. M., Baltus, B., Huizinga, T. W. J., Pieterman, E., Fero, M., et al. (2005) · Arthritis & Rheumatism · doi:10.1002/art.20811 · Cited by 148
Tiganescu, A., Walker, E. A., Hardy, R. S., Mayes, A. E., & Stewart, P. M. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2010.257 · Cited by 122
A short field guide to fibroblast function in immunity
Buechler, M. B., & Turley, S. J. (2018) · Seminars in Immunology · doi:10.1016/j.smim.2017.11.001 · Cited by 121
On markov blankets and hierarchical self-organisation
Palacios, E. R., Razi, A., Parr, T., Kirchhoff, M., & Friston, K. (2020) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2019.110089 · Cited by 115
Tumor-Secreted LOXL2 Activates Fibroblasts through FAK Signaling
Barker, H. E., Bird, D., Lang, G., & Erler, J. T. (2013) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-13-0033-t · Cited by 119
Tomo-Seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury
Lacraz, G. P. A., Junker, J. P., Gladka, M. M., Molenaar, B., Scholman, K. T., Vigil-Garcia, M., Versteeg, D., de Ruiter, H., Vermunt, M. W., Creyghton, M. P., et al. (2017) · Circulation · doi:10.1161/circulationaha.117.027832 · Cited by 111
Mia, M. M., Boersema, M., & Bank, R. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091559 · Cited by 109
Epidermal patterning and induction of different hair types during mouse embryonic development
Duverger, O., & Morasso, M. I. (2009) · Birth Defects Research Part C: Embryo Today: Reviews · doi:10.1002/bdrc.20158 · Cited by 102
Cardiac fibroblasts: more than mechanical support
Doppler, S. A., Carvalho, C., Lahm, H., Deutsch, M.-A., Dreßen, M., Puluca, N., Lange, R., & Krane, M. (2017) · Journal of Thoracic Disease · doi:10.21037/jtd.2017.03.122 · Cited by 86
Zhou, W., Xu, G., Wang, Y., Xu, Z., Liu, X., Xu, X., Ren, G., & Tian, K. (2017) · Cell Cycle · doi:10.1080/15384101.2016.1252882 · Cited by 76
Fibroblasts: Diverse Cells Critical to Biomaterials Integration
Hannan, R. T., Peirce, S. M., & Barker, T. H. (2018) · ACS Biomaterials Science & Engineering · doi:10.1021/acsbiomaterials.7b00244 · Cited by 59
Pemberton, H., Anderton, E., Patel, H., Brookes, S., Chandler, H., Palermo, R., Stock, J., Rodriguez-Niedenführ, M., Racek, T., de Breed, L., et al. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r23 · Cited by 50
Rita Lecca, M., Wagner, U., Patrignani, A., Berger, E. G., & Hennet, T. (2005) · The FASEB Journal · doi:10.1096/fj.04-2397fje · Cited by 48
Targeting the stromal microenvironment in chronic inflammation
FILER, A., PITZALIS, C., & BUCKLEY, C. (2006) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2006.03.007 · Cited by 45
Anatomic Demarcation of Cells: Genes to Patterns
Chang, H. Y. (2009) · Science · doi:10.1126/science.1175686 · Cited by 45
Self-citationBET bromodomain proteins regulate transcriptional reprogramming in genetic dilated cardiomyopathy
Antolic, A., Wakimoto, H., Jiao, Z., Gorham, J. M., DePalma, S. R., Lemieux, M. E., Conner, D. A., Lee, D. Y., Qi, J., Seidman, J. G., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.138687 · Cited by 41
Pruett, N. D., Hajdu, Z., Zhang, J., Visconti, R. P., Kern, M. J., Wellik, D. M., Majesky, M. W., & Awgulewitsch, A. (2012) · Biology Open · doi:10.1242/bio.2012039 · Cited by 26
M. S. Barron, A., Fabre, T., & De, S. (2024) · F1000Research · doi:10.12688/f1000research.143472.1 · Cited by 8
Metadata
- Authors
- Chang, H. Y., Chi, J.-T., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., & Brown, P. O.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2002-09-24
- Volume
- 99
- Issue
- 20
- Pages
- 12877-12882
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W1996994627
- Cited by
- 1,151
- References
- 3
- FWCI
- 7.67
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.