Publications

Latest publications

Publications

2026

A scalable MNase-seq framework for reproducible nucleosome profiling across pluripotent stem cell and cardiomyocyte models. Thekkedam, C., Humphreys, D. T., Naval-Sanchez, M., Nicks, A. M., Harvey, R. P., & Contreras, O.* (2026) Computational Structural Biotechnology Journal. 35(1), 0204. https://doi.org/10.34133/csbj.0204 *Corresponding author

Multi-omic analysis of human PHACTR1 signaling networks. Wolhuter K., Ma L., Bryce NL., Contreras O., Mellett N., Zhong L., Giles C, Harvey RP., Björkegren J.L.M., Meikle P., Kovacic J.C. Communications Biology 9, 265 (2026). https://doi.org/10.1038/s42003-026-09542-w

Proteo-transcriptomics and morphometrics of teleost cardiac cells define regulatory networks and exercise-induced cardiomyocyte hypertrophy and hyperplasia. Contreras, O.*, Smith, G., Santiago, C.F., Dey, M., Thekkedam, C., Chand, R., Gonzalez-Rajal, A., Zhong, L., Wong, E., Fatkin, D., Harvey, RP. bioRxiv 2026.01.11.698907; doi: https://doi.org/10.64898/2026.01.11.698907 *Corresponding author

2025

OpenEMMU: a versatile, open-source EdU multiplexing methodology for studying DNA replication and cell cycle dynamics. Contreras O.*, Thekkedam C., Zaunders J., Aguirre-MacLennan I., Murray N.J., Gonzalez Cordero A., Harvey R.P.* iScience, 28(9), 113380. https://doi.org/10.1016/j.isci.2025.113380

*Corresponding authors

D Fatkin, C Santiago, O Contreras, R Chand, J Cvetkovska, G Trivedi, C Thekkedam, D Palipana, I Huttner, R Harvey, Regular swim exercise improves cardiac function in a zebrafish model of TTNtv-related dilated cardiomyopathy, European Heart Journal, Volume 46, Issue Supplement_1, November 2025, ehaf784.4770, https://doi.org/10.1093/eurheartj/ehaf784.4770

2024

Targeting de novo lipogenesis improves gemcitabine efficacy in pancreatic ductal adenocarcinoma. Sarah E Hancock, Linda Garthwaite, Konstantina Harellis, Michael Susetio, Eileen Ding, Laura Choong, Osvaldo Contreras, Amy Nguyen, Josiah Lising, Felicia KM Hansen, Puttandon Wongsomboon, Jan Philipp Menzel, Berwyck LJ Poad, Todd W Mitchell, Stephen J Blanksby, Nigel Turner. bioRxiv 2024.12.18.628624; doi: https://doi.org/10.1101/2024.12.18.628624 

Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis across diverse cardiovascular pathologies. Patrick, R., Janbandhu, V., Tallapragada, V., Tan, S. S. M., McKinna, E. E., Contreras, O., Ghazanfar, S., Humphreys, D. T., Murray, N. J., Tran, Y. T. H., Hume, R. D., Chong, J. J. H., & Harvey, R. P. (2024). Science Advances, 10(25), eadk8501. https://doi.org/10.1126/sciadv.adk8501

Interactive data portal that allows users to examine gene expression at the single-cell level in cardiac fibroblasts: https://lnkd.in/gwb86jJV

Fibro-adipogenic progenitors in physiological adipogenesis and intermuscular adipose tissue remodeling.

Flores-Opazo, M., Kopinke, D., Helmbacher, F., Fernández-Verdejo, R., Tuñón-Suárez, M., Lynch, G. S., & Contreras, O#. (2024). Molecular Aspects of Medicine, 97, 101277. https://doi.org/10.1016/j.mam.2024.101277 #Lead and corresponding author

Tumour Biomechanics Alters Metastatic Dissemination of Triple Negative Breast Cancer via Rewiring Fatty Acid Metabolism.

Filipe, E., …, Contreras, O., …, Cox, T. Advanced Science. 2024, 2307963. https://doi.org/10.1002/advs.202307963

2023

Clinical Pathway for Coronary Atherosclerosis in Patients Without Conventional Modifiable Risk Factors: JACC State-of-the-Art Review. Figtree, G, Vernon, S, Harmer, J. et al. (CRE for CAD Collaborators). J Am Coll Cardiol. 2023 Sep, 82 (13) 1343–1359. https://doi.org/10.1016/j.jacc.2023.06.045

Development of a robust induced pluripotent stem cell atrial cardiomyocyte differentiation protocol to model atrial arrhythmia. Thorpe, J., Perry, M.D., Contreras, O., Hurley, E., Parker, G., Harvey, R.P., Hill, A.P., Vandenberg, J.I. Stem Cell Res Ther. Jul 27;14(1):183. doi: 10.1186/s13287-023-03405-5. PMID: 37501071; PMCID: PMC10373292. 

Single-Cell Transcriptome Dynamics of the Autotaxin-Lysophosphatidic Acid Axis During Muscle Regeneration Reveal Proliferative Effects in Mesenchymal Fibro-Adipogenic Progenitors. Contreras, O.* & Harvey P., R. (2023) Front. Cell Dev. Biol. Sec. Molecular and Cellular Pathology, Volume 11 - 2023 | doi: 10.3389/fcell.2023.1017660 *Corresponding author

2022

Temporal transcriptomic dynamics of the ATX-LPAR-PLPP axis during skeletal muscle regeneration at single cell resolution. Contreras, O.* (2022) bioRxiv https://doi.org/10.1101/2022.07.02.498539 *Corresponding author

Cardiac fibroblast heterogeneity and dynamics through the lens of single cell dual ‘omics. Harvey, R.P., Patrick, R., Janbandhu, V., and Contreras, O. (2022) Cardiovascular Research, cvac037, 1-3,  https://doi.org/10.1093/cvr/cvac037 Invited Editorial

Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction. Janbandhu, V., Tallapragada, V., Patrick, R., Li, Y., Abegunawardena, D., Humphreys, D.T., Martin, E.M.M.A., Ward, A.O., Contreras, O., Farbehi, F., Yao, E., Du, Y., Dunwoodie, S.L, Bursac, N., Harvey, R.P. (2022) Cell Stem Cell 29, 1–17. https://doi.org/10.1016/j.stem.2021.10.009 

2021

Origins, potency, and heterogeneity of skeletal muscle fibro-adipogenic progenitors—time for new definitions. Contreras, O.*, Rossi, F.M.V. & Theret, M*. (2021) Skeletal Muscle 11, 16 https://doi.org/10.1186/s13395-021-00265-6 *Corresponding authors. Invited Review

PDGF-PDGFR network differentially regulates myogenic cell fate, migration, proliferation, and cell cycle progression. Contreras, O.*, Cordova-Casanova, A., Brandan, E. (2021) Cellular Signalling. https://www.sciencedirect.com/science/article/pii/S089865682100125X *Corresponding author.

Evolving Roles of Muscle-Resident Fibro-Adipogenic Progenitors in Health, Regeneration,  Neuromuscular Disorders, and Aging. Theret, M.*, Rossi, F. M. V, & Contreras, O.* (2021). Frontiers in Physiology. doi: 10.3389/fphys.2021.673404 https://doi.org/10.3389/fphys.2021.673404 *Corresponding authors.

In vitro assessment of anti-fibrotic activity does not predict their in vivo efficacy in murine models of Duchenne muscular dystrophy. Theret, M., Low, M., Rempel, L., Li, F. F., Tung, L. W., Contreras, O., Chang, C., Wu, A., Soliman, H., Rossi, F. M. V. (2021) Life Sciences. https://doi.org/10.1016/j.lfs.2021.119482

2020

Single-cell revolution unveils the mysteries of the regenerative mammalian digit tip. (2020) Riquelme-Guzmán, C. & Contreras, O*. Developmental Biology. *Corresponding author. https://doi.org/10.1016/j.ydbio.2020.02.002

Hic1 deletion unleashes quiescent connective tissue stem cells and impairs skeletal muscle regeneration. (2020) Contreras, O*. Journal of Cell Communication and Signaling. *Corresponding author. https://doi.org/10.1007/s12079-019-00545-3

2020

TGF-β-driven downregulation of the transcription factor TCF7L2 affects Wnt/β-catenin signaling in PDGFRα+ fibroblasts. Contreras, O.*, Soliman, H., Theret, M., Rossi, F. M. V, & Brandan, E.* (2020). Journal of Cell Science, 133(12), jcs242297. https://doi.org/10.1242/jcs.242297 *Corresponding authors.

2019

Cross-talk between TGF-β and PDGFRα signaling pathways regulates the fate of stromal fibro-adipogenic progenitors. (2019). Contreras O.*, Cruz-Soca M., Theret M., Soliman H.,  Tung L. W., Groppa E., Rossi F. M., Brandan E.* Journal of Cell Science. 132, 232157. doi:10.1242/jcs.232157 *Corresponding authors.

Adherent muscle connective tissue fibroblasts are phenotypically and biochemically equivalent to stromal fibro/adipogenic progenitors. (2019). Contreras, O., Rossi, F. M., Brandan, E. Matrix Biology Plus. https://doi.org/10.1016/j.mbplus.2019.04.003

Denervation-induced skeletal muscle fibrosis is mediated by CTGF/CCN2 independently of TGF-β. (2019). Rebolledo D.L., González D., Faundez-Contreras J., Contreras, O., Vio C.P., Murphy-Ullrich J.E., Lipson K.E., Brandan E. Matrix Biology. https://doi.org/10.1016/j.matbio.2019.01.002

2018

Nilotinib impairs skeletal myogenesis by increasing myoblast proliferation. (2018). Contreras, O., Villarreal, M., Brandan, E. Skeletal Muscle. https://doi.org/10.1186/s13395-018-0150-5

Expression of CTGF/CCN2 in response to LPA is stimulated by fibrotic extracellular matrix via the integrin/FAK axis. (2018). *Riquelme-Guzmán C., *Contreras, O., Brandan, E. American Journal of Physiology-Cell Physiology. https://doi.org/10.1152/ajpcell.00013.2017 *Both authors contributed equally.

2017

ALS skeletal muscle shows enhanced TGF-β signaling, fibrosis and induction of fibro/adipogenic progenitor markers. (2017). Gonzalez D., Contreras O., Rebolledo D.L., Espinoza JP., van Zundert B., Brandan E. Plos ONE. https://doi.org/10.1371/journal.pone.0177649

Fibro/adipogenic progenitors safeguard themselves: a novel mechanism to reduce fibrosis is discovered. (2017). Contreras O., Brandan E. Journal of Cell Communication and Signaling. https://doi.org/10.1007/s12079-016-0372-4

2016

Connective tissue cells expressing fibro/adipogenic progenitor markers increase under chronic damage: relevance in fibroblast-myofibroblast differentiation and skeletal muscle fibrosis. (2016). Contreras O., Rebolledo D.L., Oyarzún JE., Olguín H.C., Brandan O. Cell Tissue Res. https://doi.org/10.1007/s00441-015-2343-0

2013-2015

RECK-Mediated β1-Integrin Regulation by TGF-β1 Is Critical for Wound Contraction in Mice. (2015). Gutiérrez J., Droppelmann C.A., Contreras O., Takahashi C., Brandan E. Plos ONE. https://doi.org/10.1371/journal.pone.0135005

Transforming growth factor type-β inhibits Mas receptor expression in fibroblasts but not in myoblasts or differentiated myotubes; Relevance to fibrosis associated to muscular dystrophies. (2015). Cofre C., Acuña MJ., Contreras O., Morales MG., Riquelme C., Bader M., Santos R., Cabello-Verrugio C., Brandan E. BioFactors. https://doi.org/10.1002/biof.1208

Undergraduate Publications

Syndecan 4 interacts genetically with Vangl2 to regulate neural tube closure and planar cell polarity. (2013). Escobedo, N., Contreras, O., Muñoz, R., Farías, M., Carrasco, H., Hill, C., … Larraín, J. Development, 140(14). https://doi.org/10.1242/dev.091173

BioRxiv (pre-print, open access)

2022

Temporal transcriptomic dynamics of the ATX-LPAR-PLPP axis during skeletal muscle regeneration at single cell resolution. Contreras, O.* (2022) bioRxiv https://doi.org/10.1101/2022.07.02.498539 *Corresponding author

2021

Targeting fibrosis in the Duchenne Muscular Dystrophy mice model: an uphill battle. (2021) Theret, M.*, Low, M.*, Rempel, L. Li, F., Tung, L. W., Contreras, O., Chang, C., Wu, A., Soliman, H., Rossi, F. M. V#.  bioRxiv, p. 2021.01.20.427485. doi: 10.1101/2021.01.20.427485. https://www.biorxiv.org/content/10.1101/2021.01.20.427485v1 

2020

TGF-β-driven downregulation of the Wnt/β-Catenin transcription factor TCF7L2/TCF4 in PDGFRα+ fibroblasts. Contreras, O.*, Soliman, H., Theret, M., Rossi, F. M. V., Brandan E.*(2020) bioRxiv https://doi.org/10.1101/2020.01.05.895334 *Both corresponding authors.