June update: New IBD project launched!

Your monthly run-down of Open Targets happenings is here!

Two hugely exciting Open Targets papers were published last month. Ludovic Vallier explored the mechanisms of liver regeneration in chronic disease, and Ana Cvejic built an immune atlas of lung cancer. Congratulations to both teams!

In May we also celebrated World IBD Day, launching a new project: Open-IBD. This is one of several projects recently launched, including the Perturbation Catalogue — for which we are recruiting!

Laying out the picnic blanket,

Helena

Exploring mechanisms of liver repair to pave the way for regenerative therapies

Ludovic Vallier's work on liver regeneration in chronic disease is out now in Nature!

The study found that chronic injury creates an environment that induces cellular plasticity, bringing us one step closer on the path to regenerative therapies. Using single-cell analyses on biopsies from patients with Metabolic Dysfunction-Associated Steatotic Liver Disease, Vallier and his team showed that the liver can repair itself when chronically injured, but this regenerative process may also result in progression toward cancer.

Building an immune atlas of lung cancer to map tumour microenvironements

In the largest single-cell multiomics analysis of treatment-naïve non-small cell lung cancer (NSCLC) patients, Ana Cvejic and her team built an immune atlas to uncover the role of myeloid cells within NSCLC tumours.

The work was part of an Open Targets project, in close collaboration with industry scientists.

“This atlas provides key insights into the tumour microenvironment in non-small cell lung cancers (...). It’s an excellent foundation to inform our drug discovery initiatives and dig into the biology of potential new targets,” says Angela Hadjipanayis, Head of Disease Profiling Genomics & Flow Cytometry Precision Medicine and Computational Biology at Sanofi.

We interviewed Ana about the work — read the article on the Open Targets blog.

Uncovering IBD disease biomarkers for personalised medicine

On World IBD Day, we launched a new Open Targets project: Open-IBD, a longitudinal multi-omics inception cohort in inflammatory bowel disease.

Carl Anderson, Open-IBD Scientific Lead, made a short video to announce the project.

”Our goal with Open-IBD is to work with patients to uncover biomarkers that can be used to guide personalised treatment, helping to understand why IBD impacts people in different ways, and to provide new and tailored options to those living with this condition,” says Chris Lamb, Open-IBD Clinical Lead from Newcastle University and Honorary Consultant in Gastroenterology at Newcastle Hospitals.

”We have launched Open-IBD at a crucial time where the treatment landscape of IBD is changing, and believe that this ambitious project can make a real difference for patients and the future of IBD management.”

Read the full press release.

Can you help us build the Perturbation Catalogue?

What is the impact of modifying genes and proteins? Open Targets is developing the Perturbation Catalogue, bringing together harmonised and curated human gene, variant, and expression data, to provide a systematic and comprehensive answer to this question. The open-source Perturbation Catalogue will integrate data from functional genetics screens and post-perturbational experiments, including data from CRISPR, MAVE, and Perturb-seq, and will deliver gold standard machine learning-ready datasets, and a highly customisable public cloud platform with distributed data warehousing technology for cross metadata queries.

Help us build this! The project is currently recruiting a postdoc and a full stack developer — see the job postings below for more information.

Interested in joining Open Targets? We are currently recruiting:

• Postdoc in CRISPR Meta-Analytics and AI for Therapeutic Target Discovery and Prioritisation (14 June) — As part of the Perturbation Catalogue project, extend existing algorithms and tools, and design and implement novel methods to support data analysis, curation, interpretation, and exploitation for target discovery and prioritisation. The position is based in the lab of Francesco Iorio at the Human Technopole.

• Senior Full Stack Developer (30 June) — Support and develop software to handle programmatic access and a portal interface to explore, combine, visualise and access a wealth of perturbation data. This will enable the extension and application of existing algorithms and the design of new computational methods for functional genetics and target identification and prioritisation, offering enhanced statistical power and the capability to work with disease subtypes at a finer granularity. This position is based at EMBL’s European Bioinformatics Institute.

Keep an eye on our jobs page for all our opportunities.

I’d love to know what you think of this newsletter — let me know by commenting or emailing [email protected]!

— Helena, Open Targets Communications Lead