I am a postdoctoral researcher in
the Glioma Genomics group at Leeds Institute of Medical Research (LIMR). The main focus of my work, which is funded by
The Brain Tumour Charity, is to understand how glioblastoma (GBM) brain tumours
acquire resistance to treatment, leading 100% of primary tumours to recur. The two
working hypotheses of our group are that either individual subclones from the
primary tumour are inherently resistant and selected for during treatment, or that
transcriptional reprogramming enables cells to adapt their phenotype and become
To understand more about the
mechanism of resistance in GBM, I am using a novel technique known as
nanobiopsy that allows us to extract cytoplasmic material from single brain
tumour cells without killing them. Using this technique we can now, for the
first time, longitudinally track and biopsy single cells sequentially during
treatment, thereby characterising how the transcriptional profile of individual
cells change. To achieve this, I am sequencing sub-single cell RNAseq
libraries, created from cytoplasm nanobiopsied pre and post treatment, using
the SMART-seq2 and NEXTeraXT workflow.
The biggest challenge that had to
be overcome was the amplification of such small amounts of RNA (<1pg) into
adequate cDNA for use in NGS library preparation. Dr Iain Macaulay, at the
Earlham Institute, assisted with this part of the project. By acquiring a travel
grant by the Harold Hyam Wingate Foundation, I was able to visit his state-of-the-art
laboratory and worked closely with experts in his single cell technology group
to optimise the SMART-seq2 protocol for ultra-low RNA amounts. We have
successfully obtained sufficient amounts of cDNA for downstream library
preparation, from a starting material of as low as 0.5pg of RNA (approx. 5-10%
of a cell’s RNA).
Apart from achieving our very
challenging aim, my visit to the Earlham Institute was very inspiring. I spent
time preparing RNAseq libraries using different robots, I learnt a quick and
easy way to check the sorting alignment on FACS Melody prior to sorting, and I
have brainstormed and discussed other alternative ways of amplifying the
nanobiopsies in order to get information beyond the coding RNA species.
Keeping our commitment to update and strengthen our
skills on Omics data analyses, our
Bioinformatics Research Officer, Dr Elton Vasconcelos, has recently attended a
Proteomics Bioinformatics Course provided by EMBL-EBI jointly with the Wellcome
Genome Campus Advanced Courses at Hinxton, UK. The course included a mix of
both theoretical lectures and practical sessions aimed at hands-on training in the basics of mass
spectrometry and proteomics bioinformatics, search engines and post-processing
software, quantitative approaches, MS data repositories, the use of public
databases for protein analysis, annotation of subsequent protein lists and incorporation
of information from molecular interaction and pathway databases.
Dr Vasconcelos has identified proteomics as one of the key omics approaches that he wants to develop further expertise in. He hugely benefitted from attending the EBML-EBI course, improving his understanding of the data, as well as how to better perform analyses using cutting-edge tools. He has already started collaborating on proteomics data analysis efforts for different projects in both Dr Julie Aspden and Dr Niamh Forde research groups. His background in molecular biology/biochemistry and bioinformatics definitely helps him making the most of this new skill acquisition, enabling him to enhance a niche skill set within LeedsOmics.
The LeedsOmics Research Symposium 2019 on May 13th,
2019 was a great success again this year, full of great talks by talented
researchers with an emphasis on genomics, transcriptomics, translatomics and
proteomics at the University of Leeds. We hosted two keynote speakers: Dr
Michael Barnes (Queen Mary University of London) and Prof Claire Eyers
(University of Liverpool), who delighted us with fantastic overviews on machine
learning applied to omics-derived clinical data and paradigm shifts in our
understanding of protein phosphorylation, respectively. Attendees (PhD
students, postdocs, technicians, and academics) had plenty of opportunities to
chat about omics-related science during coffee/lunch breaks, a stimulating
poster session, and wine and cheese reception.
Congratulations to Alysha Taylor on winning the best oral presentation award and to Ioannis Tsagakis on winning the best poster presentation award at LeedsOmics Research Symposium 2019.
This morning we celebrated the launch of Leeds Omics. We had well over 100 members of the community share in the celebration with us, including our two Deans (as photographed). It was a great opportunity for us to share our vision for Leeds Omics and for us all to get to meet one another and start the development of this hugely energetic research community.
We would like to thank all those members of the community that showed their support and interest in coming along today, and our two Deans for their words of encouragement and support.
We have an exciting and busy time ahead as we begin our various community building activities over the coming weeks and months. We really look forward to meeting you all to discuss research !
Leeds Omics is a cross faculty initiative between the Faculty of Biological Sciences and the Faculty of Medicine and Heath Sciences. The aim is to bring together the critical mass of researchers using the omics technologies across the University of Leeds (www.leedsomics.org). The launch will take place in LIDA on level 11 of the Worsley building on Tuesday the 21st of June at 10.00am. Both John Ladbury (Dean of FBS) and Paul Stewart (Dean of FMH) will be saying a few words to celebrate the launch, and we will give a short overview of the vision for Leeds Omics. Please join us for coffee and cake, and a chance to network with other researchers using or interested in using omics data and technologies here at Leeds.
To subscribe to our mailing list please click the link below:
If you are a PI and are interested in being a member of Leeds Omics (including having your research profile on the Leeds Omics website) please e-mail a member of the Leeds Omics steering committee (J.Aspden@leeds.ac.uk:M.OConnell@leeds.ac.uk: N.Forde@leeds.ac.uk) and we will give you the information that we need.
Looking forward to seeing you there!
Niamh, Mary and Julie (Leeds Omics steering committee).