Tell me what your proteome is and I’ll tell you what you are: the proteomic maps of 949 human cancer cell lines
Emanuel Gonçalves — INESC-ID Automated Reasoning and Software Reliability (ARSR) computational biology researcher — has published a groundbreaking study in the journal Cancer Cell (published online 14 July 2022).
In the article Pan-cancer proteomic map of 949 human cell lines, the last study resulting from Gonçalves’ postdoctoral work at the Wellcome Sanger Institute, Gonçalves — together with co-first authors Rebecca C. Poulos and Zhaoxiang Cai and an immense and interdisciplinary group of colleagues — addressed one substantial gap in cancer research: until now a comprehensive characterization of the proteomes of cancer cells was lacking, an absence that substantially limited the identification of novel cancer biomarkers (the molecular signature that each tumour produces).
To tackle this challenge, the team profiled the proteomes — the complete set of proteins expressed by a genome — of 949 cancer cell lines from 28 different tissues using mass spectrometry (a technique used to identify individual molecules in a complex solution based on their unique mass-to-charge signature). Then, analysing some 8,498 proteins within an integrated strategy bringing together multi-omics with drug response and the CRISPR-Cas9 gene editing technology (to manipulate the expression of genes one by one and look at how essential each of the respectively expressed proteins was), Gonçalves and his colleagues revealed thousands of protein biomarkers of cancer vulnerabilities (those molecular changes that promote tumour development and progression, such as those in genes responsible for cell proliferation).
“This study significantly expands our molecular knowledge of cancer cells — more than doubling the number of cancer cell lines with proteomes characterized so far — and of protein regulation in cancer,” Gonçalves shared with us. “Complementing genomics, this dataset provides unique information only captured at the protein level, which we would be missing otherwise, with several important applications, from more accurate therapeutic biomarkers to unique insights into protein associations.”
A study of this dimension, technical complexity and impact inevitably results in game-changing and novel ways of looking at cancer diagnosis, study and potential treatments. As Gonçalves reminded us, “As part of the Cancer DepMap effort, this enables a proteomic lookup map to study cancer, from identifying potential therapeutic biomarkers to studying fundamental processes of protein regulation. This will hopefully become an important resource for the broad community.” Importantly, this pan-cancer proteomic map (ProCan-DepMapSanger), an invaluable resource, is already available online.
And how is Gonçalves’ future research progressing from this major paper? “Looking forward, I’m interested in continuing the work of harnessing these large scale datasets and their integration. There are biological mechanisms that can only be studied and understood when taking a holistic approach integrating multiple molecular datasets, like the one we present here.”
Interdisciplinarity is key in tackling the biggest challenges in contemporary biomedical science. The joining together of computational and molecular biology approaches represents one such unique hope — that of fully tackling the emperor of all maladies.
Research data repositories and tools for human genomics data sharing
Inform the human research community of the status and availability of BioData.pt Local EGA and discuss its need and usability challenges.
The European Genome-phenome Archive (EGA) is a repository for all sequence and genotype experiment types, including case-control, population, and family studies. The EGA will serve as a permanent archive that will archive several levels of data, including the raw data (which could, for example, be re-analysed in the future by other algorithms) as well as the genotype calls provided by the submitters.
Responding to national regulations over human data sharing and other constraints, BioData.pt deploys and operates a Local EGA instance and tools that allow data discovery of genomic and phenoclinic data, following the GA4GH standard and international best practices.
This workshop aims at informing the human research community of the status and availability of BioData.pt Local EGA and discuss from several perspectives its need and usability challenges.
Further details and registration are available here.
OLISSIPO Summer School in Lisbon | Computational phylogenetics to analyse the evolution of cells and communities
We are happy to announce the OLISSIPO Summer School on Computational phylogenetics to analyse the evolution of cells and communities, which will be held in Lisbon, Portugal, at INESC-ID, between July 2-7, 2023.
David Posada, University of Vigo (class)
João Alves, University of Vigo (hands-on)
Nadia El-Mabrouk, Université de Montréal (class)
Mattéo Delabre, Université de Montréal (hands-on)
Ran Libeskind-Hadas, Claremont McKenna College (class and hands-on)
Russell Schwartz, Carnegie Mellon University (class and hands-on)
See the preliminary agenda at: https://olissipo.inesc-id.pt/tree-tango-school
Registration is mandatory. You can register at: https://forms.gle/VsASFHW5E7MJvaCc9
The registration fee is 250€ for students and OLISSIPO members and 350€ for postdocs or other researchers (meals indicated at the schedule of the school are included, accommodation and flights are not). All details will be made available upon registration.
We will have slots for flash talks (3-10 min depending on the number of submissions) to present yourself and the work you have been developing in your research.
The 13th Lisbon Machine Learning School | LxMLS 2023
The Lisbon Machine Learning Summer School (LxMLS) takes place yearly at Instituto Superior Técnico (IST). LxMLS 2023 will be a 6-day event (14-20 July, 2023), scheduled to take place as an in-person event.
The school covers a range of machine learning topics, from theory to practice, that are important in solving natural language processing problems arising in different application areas. It is organized jointly by Instituto Superior Técnico (IST), a leading Engineering and Science school in Portugal, the Instituto de Telecomunicações, the Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa (INESC-ID), the Lisbon ELLIS Unit for Learning and Intelligent Systems (LUMLIS), Unbabel, Zendesk, and IBM Research.
Check online for information about past editions: LxMLS 2011, LxMLS 2012, LxMLS 2013, LxMLS 2014, LxMLS 2015, LxMLS 2016, LxMLS 2017, LxMLS 2018, LxMLS 2019, LxMLS 2020, LxMLS 2021, LxMLS 2022 (you can also watch the videos of the lectures for 2016, 2017, 2018, and 2020).
31st International Conference on Information Systems Development (ISD 2023)
The 31st International Conference on Information Systems Development (ISD 2023) conference provides a forum for research and developments in the field of information systems. The theme of ISD 2023 is “Information systems development, organizational aspects and societal trends”. New trends in developing information systems emphasize the continuous collaboration between developers and operators in order to optimize the software delivery time. The conference promotes research on methodological and technological issues and how IS developers and operators are transforming organizations and society through information systems.
The ISD 2023 conference held this year also provides an opportunity for researchers and practitioners to promote their research, practical experience, and to discuss issues related to Information Systems through papers, posters, and journal-first paper presentations.
ISD 2023 will be hosted by Instituto Superior Técnico, in Lisbon, Portugal, on August 30–September 1, 2023.