Jiannis Ragoussis

Dr. Jiannis Ragoussis

McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
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Research Focus & Metrics

Academic Career Length

29Years (1998-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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8 July 2020 in Nature Communications
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CCCharles P. Couturier
Charles P. Couturier
SAShamini Ayyadhury
Shamini Ayyadhury
PLPhuong U. Le
Phuong U. Le
JNJavad Nadaf
Javad Nadaf
JMJean Monlong
Jean Monlong
KPKevin Petrecca
Kevin Petrecca
Cancer stem cells are critical for cancer initiation, development, and treatment resistance. Our understanding of these processes, and how they relate to glioblastoma heterogeneity, is limited. To overcome these limitations, we performed single-cell RNA sequencing on 53586 adult glioblastoma cells and 22637 normal human fetal brain cells, and compared the lineage hierarchy of the developing human brain to the transcriptome of cancer cells. We find a conserved neural tri-lineage cancer hierarchy centered around glial progenitor-like cells. We also find that this progenitor population contains the majority of the cancer’s cycling cells, and, using RNA velocity, is often the originator of the other cell types. Finally, we show that this hierarchal map can be used to identify therapeutic targets specific to progenitor cancer stem cells. Our analyses show that normal brain development reconciles glioblastoma development, suggests a possible origin for glioblastoma hierarchy, and helps to identify cancer stem cell-specific targets.

27 April 2020 in Nature Neuroscience
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CNCorina Nagy
Corina Nagy
MMMalosree Maitra
Malosree Maitra
ATArnaud Tanti
Arnaud Tanti
MSMatthew Suderman
Matthew Suderman
JTJean-Francois Théroux
Jean-Francois Théroux
GTGustavo Turecki
Gustavo Turecki

25 November 2019 in Nature Genetics
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SJSelin Jessa
Selin Jessa
ABAlexis Blanchet-Cohen
Alexis Blanchet-Cohen
BKBrian Krug
Brian Krug
MVMaria Vladoiu
Maria Vladoiu
MCMarie Coutelier
Marie Coutelier
CKClaudia L. Kleinman
Claudia L. Kleinman

11 February 2022 in Nature Communications
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STShannon Tansley
Shannon Tansley
SUSonali Uttam
Sonali Uttam
AGAlba Ureña Guzmán
Alba Ureña Guzmán
MYMoein Yaqubi
Moein Yaqubi
APAlain Pacis
Alain Pacis
AKArkady Khoutorsky
Arkady Khoutorsky
Activation of microglia in the spinal cord following peripheral nerve injury is critical for the development of long-lasting pain hypersensitivity. However, it remains unclear whether distinct microglia subpopulations or states contribute to different stages of pain development and maintenance. Using single-cell RNA-sequencing, we show that peripheral nerve injury induces the generation of a male-specific inflammatory microglia subtype, and demonstrate increased proliferation of microglia in male as compared to female mice. We also show time- and sex-specific transcriptional changes in different microglial subpopulations following peripheral nerve injury. Apolipoprotein E (Apoe) is the top upregulated gene in spinal cord microglia at chronic time points after peripheral nerve injury in mice. Furthermore, polymorphisms in the APOE gene in humans are associated with chronic pain. Single-cell RNA sequencing analysis of human spinal cord microglia reveals a subpopulation with a disease-related transcriptional signature. Our data provide a detailed analysis of transcriptional states of mouse and human spinal cord microglia, and identify a link between ApoE and chronic pain in humans.

24 August 2016 in Scientific Reports
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Journal Article
Open access
SOSpyros Oikonomopoulos
Spyros Oikonomopoulos
YWYu Chang Wang
Yu Chang Wang
HDHaig Djambazian
Haig Djambazian
DBDunarel Badescu
Dunarel Badescu
JRJiannis Ragoussis
Jiannis Ragoussis
To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.

22 December 2013 in EMBO Reports
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HCHani Choudhry
Hani Choudhry
JSJohannes Schödel
Johannes Schödel
SOSpyros Oikonomopoulos
Spyros Oikonomopoulos
CCCarme Camps
Carme Camps
SGSteffen Grampp
Steffen Grampp
DMDavid R. Mole
David R. Mole
Hypoxia is central to both ischaemic and neoplastic diseases. However, the non‐coding transcriptional response to hypoxia is largely uncharacterized. We undertook integrated genomic analyses of both non‐coding and coding transcripts using massively parallel sequencing and interfaced this data with pan‐genomic analyses of hypoxia‐inducible factor (HIF) and RNApol2 binding in hypoxic cells. These analyses revealed that all classes of RNA are profoundly regulated by hypoxia and implicated HIF as a major direct regulator of both the non‐coding and coding transcriptome, acting predominantly through release of pre‐bound promoter‐paused RNApol2. These findings indicate that the transcriptional response to hypoxia is substantially more extensive than previously considered. ![][1] Integrated genomic analysis of the cellular response to hypoxia using massively parallel sequencing shows profound regulation of the non‐coding as well as the coding transcriptome. This report also identifies the release of pre‐bound promoter‐paused RNApol2 by hypoxia‐inducible factor (HIF) as a major effector of this transcriptional response. [1]: pending:yes