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SIOMICS

SIngle-cell multi-OMICs approach to study intra-tumour heterogeneity of soft tissue Sarcomas

Total Cost €

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EC-Contrib. €

0

Partnership

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 SIOMICS project word cloud

Explore the words cloud of the SIOMICS project. It provides you a very rough idea of what is the project "SIOMICS" about.

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Project "SIOMICS" data sheet

The following table provides information about the project.

Coordinator
THE FRANCIS CRICK INSTITUTE LIMITED 

Organization address
address: 1 MIDLAND ROAD
city: LONDON
postcode: NW1 1AT
website: www.crick.ac.uk

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country United Kingdom [UK]
 Project website https://www.crick.ac.uk/research/labs/peter-van-loo
 Total cost 195˙454 €
 EC max contribution 195˙454 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2016
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2017
 Duration (year-month-day) from 2017-04-01   to  2019-03-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    THE FRANCIS CRICK INSTITUTE LIMITED UK (LONDON) coordinator 195˙454.00

Map

 Project objective

Recently, multi-omics approaches have led to a plethora of publications describing in detail the ‘omics landscapes of common cancer types. However, at the bulk tissue level, integrating different ‘omics layers remains an uncompleted challenge. Soft tissue sarcomas are rare and often aggressive cancers of mesenchymal origin representing ~1% of all cancers but encompassing at least 50 subtypes. Hence, collecting enough of these rare samples for significant findings in a timely fashion is the biggest hurdle. This issue can be addressed by repeating observations within individual patients to generate new hypotheses. Our long-term collaboration aims to obtain the genome, transcriptome and methylome of each of 1,000 single-cells from 10 individual subtypes of soft tissue sarcomas. This design is possible thanks to DNA & RNA single-cell sequencing (SCS) of the same cell in Dr. Voet’s lab, and bespoke computational analyses in Dr. Van Loo’s lab, and access to this rare material of Prof. Flanagan, lead for the sarcoma component of the Genomics England 100,000 Genomes Project. This proposal is the pilot project, where we focus on one malignant peripheral nerve sheath tumour, a rare aggressive cancer originating from the connective tissues surrounding nerves. We will also sequence multiple regions of the primary tumour, the blood, and cell-free tumour DNA (ctDNA) before surgery and subsequently every three months. Prof. Flanagan’s group will process the samples, and Dr. Voet will oversee the sequencing. In Dr. Van Loo’s lab, I will develop the computational tools to uncover the 3 ‘omics signals at the single-cell level that are averaged out in bulk tissues. SCS will shed light on the fundamental links between cancer genomic subclones and the transcriptional and epigenetic diversity of cancer cell types; and we will answer whether ctDNA reflects the diversity of cancer cells and how it evolves in the course of treatment.

 Publications

year authors and title journal last update
List of publications.
2018 Matthew W. Fittall, William Mifsud, Nischalan Pillay, Hongtao Ye, Anna-Christina Strobl, Annelien Verfaillie, Jonas Demeulemeester, Lei Zhang, Fitim Berisha, Maxime Tarabichi, Matthew D. Young, Elena Miranda, Patrick S. Tarpey, Roberto Tirabosco, Fernanda Amary, Agamemnon E. Grigoriadis, Michael R. Stratton, Peter Van Loo, Cristina R. Antonescu, Peter J. Campbell, Adrienne M. Flanagan, Sam Behjati
Recurrent rearrangements of FOS and FOSB define osteoblastoma
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-04530-z
Nature Communications 9/1 2019-09-06
2019 Christopher D. Steele, Maxime Tarabichi, Dahmane Oukrif, Amy P. Webster, Hongtao Ye, Matthew Fittall, Patrick Lombard, Iñigo Martincorena, Patrick S. Tarpey, Grace Collord, Kerstin Haase, Sandra J. Strauss, Fitim Berisha, Heli Vaikkinen, Pawan Dhami, Marnix Jansen, Sam Behjati, M. Fernanda Amary, Roberto Tirabosco, Andrew Feber, Peter J. Campbell, Ludmil B. Alexandrov, Peter Van Loo, Adrienne M. Flanagan, Nischalan Pillay
Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways
published pages: 441-456.e8, ISSN: 1535-6108, DOI: 10.1016/j.ccell.2019.02.002
Cancer Cell 35/3 2019-09-06
2018 Maxime Tarabichi, Iñigo Martincorena, Moritz Gerstung, Armand M. Leroi, Florian Markowetz, Paul T. Spellman, Quaid D. Morris, Ole Christian Lingjærde, David C. Wedge, Peter Van Loo
Neutral tumor evolution?
published pages: 1630-1633, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0258-x
Nature Genetics 50/12 2019-09-06

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