Below you will find scientific publications authored by our members or those enabled by our platform services.
2021
Sanchez-Ferras, Oraly; Pacis, Alain; Sotiropoulou, Maria; Zhang, Yuhong; Wang, Yu Chang; Bourgey, Mathieu; Bourque, Guillaume; Ragoussis, Jiannis; Bouchard, Maxime
A coordinated progression of progenitor cell states initiates urinary tract development Journal Article
In: Nature Communications, vol. 12, no. 1, pp. 2627, 2021, ISSN: 2041-1723, (Number: 1 Publisher: Nature Publishing Group).
Abstract | Links | BibTeX | Tags: C3G, genomics, RNA-seq
@article{sanchez-ferras_coordinated_2021,
title = {A coordinated progression of progenitor cell states initiates urinary tract development},
author = {Oraly Sanchez-Ferras and Alain Pacis and Maria Sotiropoulou and Yuhong Zhang and Yu Chang Wang and Mathieu Bourgey and Guillaume Bourque and Jiannis Ragoussis and Maxime Bouchard},
url = {https://www.nature.com/articles/s41467-021-22931-5},
doi = {10.1038/s41467-021-22931-5},
issn = {2041-1723},
year = {2021},
date = {2021-01-01},
urldate = {2021-05-12},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {2627},
abstract = {The kidney and upper urinary tract develop through reciprocal interactions between the ureteric bud and the surrounding mesenchyme. Ureteric bud branching forms the arborized collecting duct system of the kidney, while ureteric tips promote nephron formation from dedicated progenitor cells. While nephron progenitor cells are relatively well characterized, the origin of ureteric bud progenitors has received little attention so far. It is well established that the ureteric bud is induced from the nephric duct, an epithelial duct derived from the intermediate mesoderm of the embryo. However, the cell state transitions underlying the progression from intermediate mesoderm to nephric duct and ureteric bud remain unknown. Here we show that nephric duct morphogenesis results from the coordinated organization of four major progenitor cell populations. Using single cell RNA-seq and Cluster RNA-seq, we show that these progenitors emerge in time and space according to a stereotypical pattern. We identify the transcription factors Tfap2a/b and Gata3 as critical coordinators of this progenitor cell progression. This study provides a better understanding of the cellular origin of the renal collecting duct system and associated urinary tract developmental diseases, which may inform guided differentiation of functional kidney tissue.},
note = {Number: 1
Publisher: Nature Publishing Group},
keywords = {C3G, genomics, RNA-seq},
pubstate = {published},
tppubtype = {article}
}
2019
Gonorazky, Hernan D; Naumenko, Sergey; Ramani, Arun K; Nelakuditi, Viswateja; Mashouri, Pouria; Wang, Peiqui; Kao, Dennis; Ohri, Krish; Viththiyapaskaran, Senthuri; Tarnopolsky, Mark A; Mathews, Katherine D; Moore, Steven A; Osorio, Andres N; Villanova, David; Kemaladewi, Dwi U; Cohn, Ronald D; Brudno, Michael; Dowling, James J
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease Journal Article
In: The American Journal of Human Genetics, vol. 104, no. 3, pp. 466–483, 2019, ISSN: 0002-9297, 1537-6605, (Publisher: Elsevier).
Links | BibTeX | Tags: diagnostics, Mendelian disease, muscular dystrophy, myotubes, RNA-seq, Transcriptomics, transdifferentiation
@article{gonorazky_expanding_2019,
title = {Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease},
author = {Hernan D Gonorazky and Sergey Naumenko and Arun K Ramani and Viswateja Nelakuditi and Pouria Mashouri and Peiqui Wang and Dennis Kao and Krish Ohri and Senthuri Viththiyapaskaran and Mark A Tarnopolsky and Katherine D Mathews and Steven A Moore and Andres N Osorio and David Villanova and Dwi U Kemaladewi and Ronald D Cohn and Michael Brudno and James J Dowling},
url = {https://www.cell.com/ajhg/abstract/S0002-9297(19)30012-6},
doi = {10.1016/j.ajhg.2019.01.012},
issn = {0002-9297, 1537-6605},
year = {2019},
date = {2019-01-01},
urldate = {2021-05-19},
journal = {The American Journal of Human Genetics},
volume = {104},
number = {3},
pages = {466--483},
note = {Publisher: Elsevier},
keywords = {diagnostics, Mendelian disease, muscular dystrophy, myotubes, RNA-seq, Transcriptomics, transdifferentiation},
pubstate = {published},
tppubtype = {article}
}
2017
Yanitch, Aymeric; Brereton, Nicholas J B; Gonzalez, Emmanuel; Labrecque, Michel; Joly, Simon; Pitre, Frederic E
Transcriptomic Response of Purple Willow (Salix purpurea) to Arsenic Stress Journal Article
In: Frontiers in Plant Science, vol. 8, 2017, ISSN: 1664-462X, (Publisher: Frontiers).
Abstract | Links | BibTeX | Tags: Abiotic stress tolerance, Arsenic, Phytoremediation, RNA-seq, Salix, Trace Elements, Transcriptomics
@article{yanitch_transcriptomic_2017,
title = {Transcriptomic Response of Purple Willow (Salix purpurea) to Arsenic Stress},
author = {Aymeric Yanitch and Nicholas J B Brereton and Emmanuel Gonzalez and Michel Labrecque and Simon Joly and Frederic E Pitre},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2017.01115/full},
doi = {10.3389/fpls.2017.01115},
issn = {1664-462X},
year = {2017},
date = {2017-01-01},
urldate = {2021-05-18},
journal = {Frontiers in Plant Science},
volume = {8},
abstract = {Arsenic (As) is a toxic element for plants and one of the most common anthropogenic pollutants found at contaminated sites. Despite its severe effects on plant metabolism, several species can accumulate substantial amounts of arsenic and endure the associated stress. However, the genetic mechanisms involved in arsenic tolerance remains obscure in many model plant species used for land decontamination (phytoremediation), including willows. The present study assesses the potential of Salix purpurea cv. ‘Fish Creek’ for arsenic phytoextraction and reveals the genetic responses behind arsenic tolerance, phytoextraction and metabolism. Four weeks of hydroponic exposure to 0, 5, 30 and 100 mg/L revealed that plants were able to tolerate up to 5 mg/L arsenic. Concentrations of 0 and 5 mg/L of arsenic treatment were then used to compare alterations in gene expression of roots, stems and leaves using RNA sequencing. Differential gene expression revealed transcripts encoding proteins putatively involved in entry of arsenic into the roots, storage in vacuoles and potential transport through the plant as well as primary and secondary (indirect) toxicity tolerance mechanisms. A major role for tannin as a compound used to relieve cellular toxicity is implicated as well as unexpected expression of the cadmium transporter CAX2, providing a potential means for internal arsenic mobility. These insights into the underpinning genetics of a successful phytoremediating species present novel opportunities for selection of dedicated arsenic tolerant crops as well as the potential to integrate such tolerances into a wider Salix ideotype alongside traits including biomass yield, biomass quality, low agricultural inputs and phytochemical production.},
note = {Publisher: Frontiers},
keywords = {Abiotic stress tolerance, Arsenic, Phytoremediation, RNA-seq, Salix, Trace Elements, Transcriptomics},
pubstate = {published},
tppubtype = {article}
}