We are EMBL: Carolin Sauer on supporting cancer research

Postdoctoral researcher Carolin Sauer is leveraging long-read sequencing to develop new detection methods for various cancers

Woman in black top standing, with arms resting on a metal bannister.
Carolin Sauer. Credits: Jeff Dowling/EMBL-EBI

The advent of new sequencing technologies has been transformative for cancer detection, unlocking innovative methods for early diagnosis and precision medicine. Advancements such as long-read sequencing provide researchers with a deeper understanding of the molecular underpinnings of cancer, paving the way for diagnostic tests and personalised treatment options. 

At EMBL’s European Bioinformatics Institute (EMBL-EBI), postdoctoral researcher Carolin Sauer is using long-read sequencing data collected from cancer patients to help create new methods for early cancer detection. In joining the Cortés-Ciriano group at EMBL-EBI, she switched fields, moving into a bioinformatics career. So far her work has gained much attention and she has recently been awarded a Marie Skłodowska-Curie Actions fellowship. Here we find out more about the impact and drivers behind Carolin’s work. 

Can you describe the work you’re doing at EMBL-EBI?

We’re developing new methods to detect cancer, particularly paediatric cancers, ovarian cancer, and brain tumours, using nanopore long-read sequencing. This technology has the potential to be more affordable, sensitive, and specific, while reducing turnaround time compared to currently used methods. Nanopore sequencing also provides a readout of the DNA methylation status – an epigenetic marker associated with gene silencing. This allows us to analyse both genomic and epigenomic data within the same assay.

Paediatric cancer detection is challenging because surgical intervention and tissue biopsies are difficult to perform on young children. Additionally, sample sizes are usually small, and there often isn’t enough tissue for pathological analysis and sequencing. Liquid biopsies – samples taken from the blood – combined with nanopore sequencing offer a less invasive method to obtain more data and information, which can be beneficial for early detection and monitoring disease progression.

How do you see your work evolving over the next few years? 

Our immediate focus is on getting the project off the ground and working with clinical collaborators to obtain donated samples. We hope to continue to grow our cohorts of samples and use machine learning and other approaches to fine-tune our detection capacity. We’d also like to explore early detection in patients who might be prone to developing cancer due to genetic predispositions, such as those suffering from Lynch syndrome – a hereditary colorectal cancer. 

There are many future benefits to moving towards using liquid biopsy sampling, including less invasive procedures and more comfortable experiences for patients. For example, patients with Lynch syndrome frequently have to undergo colonoscopies. Using nanopore sequencing on blood samples would be more comfortable and less invasive, while still providing valuable information about potential cancer development.

How important do you think collaboration is to achieving your goals?

We need clinicians to help design studies and recruit patients, and we need laboratory personnel to perform DNA extractions and sequencing. Our research wouldn’t be possible without collaboration, as we wouldn’t have any data to work with. Collaboration also helps keep the project in perspective, and ensures that our work remains relevant to the bigger picture. This is important for learning, progression, and troubleshooting. 

The supportive and collaborative environment at EMBL is also crucial to the success of our project. For example, a recent event organised across EMBL by my group leader Isidro Cortés-Ciriano brought together people from different groups to discuss their work with nanopore sequencing, the challenges they face, and the approaches they take. This exchange of knowledge and experience is valuable for all researchers involved.

Can you tell us a little bit about your Marie Skłodowska-Curie Actions fellowship and why EMBL is a great destination to carry out this fellowship?

The Marie Skłodowska-Curie Actions fellowship is part of the European Commission’s funding scheme. It’s a prestigious award for postdocs that provides an excellent opportunity to train in an area different from your PhD work, while also having a strong focus on career progression. The fellowship provides funding for salary, training, attending conferences, and some research expenses, allowing for more independence and flexibility in managing your own budget and project.

The fellowship emphasises personal development, knowledge exchange, and outreach. Applicants must outline their career aims, milestones, and the skills they need to achieve their goals. This includes participating in public engagement activities and teaching. Collaboration and public engagement are integral to the culture at EMBL, making it an exceptional organisation in which to carry out an MSCA fellowship. EMBL also offers numerous training opportunities and courses for personal growth and development, which are essential components of its postdoctoral program. These aspects are particularly valuable to me as I transition into the field of bioinformatics from a wet lab background.

What has been the biggest challenge in your career so far and how have you overcome this?

The biggest challenge for me has been gaining self-confidence and overcoming performance anxiety. I started my PhD quite young after obtaining my bachelor’s degree in biomedical sciences, and volunteering in a research lab. As I progressed through my academic journey, I encountered many talented individuals and exciting projects, which sometimes made me feel overwhelmed and doubt my abilities.

Dealing with work-related anxiety, high expectations, and perfectionism was one of the harder battles to overcome. Transitioning into a new field with less experience than my colleagues was also challenging, as it required me to trust in my abilities and give myself time to learn.

Overcoming these personal challenges is crucial for growth and success in academia. It’s essential to recognise and acknowledge these feelings and learn to manage them effectively. Openly discussing these struggles is important, as many people can relate and benefit from sharing their own stories and coping strategies.

What do you like about working at EMBL?

EMBL provides a very diverse community of colleagues. Researchers from various backgrounds and nationalities work here, which makes for a stimulating and enjoyable environment. EMBL also provides access to state-of-the-art facilities and resources, especially for genomics research.

The Wellcome Genome Campus, which is the home of EMBL-EBI, is very beautiful. The campus is well-equipped and provides a pleasant atmosphere to work in. 

Overall, EMBL is an excellent place to conduct research, offering a supportive environment for both scientific projects and personal development. 

What hobbies or interests do you have outside of work?

I enjoy rowing in Cambridge. I also have a lifelong love of ballet, although I am not currently practising due to scheduling conflicts, but I still enjoy watching ballet performances. I also picked up sewing recently, as a calming and productive way to unwind. In my free time, I’ve also been involved in the University of Cambridge Bioinformatics Training Facility, where I had the opportunity to get involved in teaching Unix command line, running pipelines for data alignment, and basic R for data tidying and visualisation, while teaching courses on the bioinformatics analysis for genomic surveillance of SARS-CoV-2 in Singapore and Trinidad and Tobago. These courses were organised by the Bioinformatics Training Facility in collaboration with UKHSA’s New Variant Assessment Platform and the World Health Organization and have been a highly enjoyable and enriching experience.

Thank you to our collaborators

Sauer’s work in the Cortés-Ciriano’s group wouldn’t be possible without the many collaborators working on these projects. These collaborators include those involved in the Stratified Medicine Paediatrics (StratMedPaeds) study: Louis Chesler, Darren Hargrave, and Michael Hubank at the Institute of Cancer Research (ICR), Andrew Beggs at the University of Birmingham, and John Anderson from UCL and Great Ormond Street Hospital for Children. Sauer and the Cortés-Ciriano group are keen to keep exploring new collaborations to expand their research and enhance understanding of cancer detection and treatment. So, if this work is of interest, please get in touch.

Tags: bioinformatics, cancer, data, data science, data sharing, embl-ebi, genomics, open access, open data, open science, oxford nanopore, sequencing, single-cell sequencing, we are embl


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