Interview: The SG-NEx project: nanopore long-read RNA-sequencing of human cancer cell lines

Webinar date: Thursday 28th February (pre-recorded on 21st February)

Time: 12pm EST/5pm GMT/9am PST

Speaker: Jonathan Göke, Genome Institute of Singapore (A*STAR)

Jonathan Göke is a Principal Investigator based at the Genome Institute of Singapore, where he uses computational genomics and transcriptomics to study cellular identity and the origin of disease. At his upcoming webinar with Technology Networks, Jonathan will be talking about his work on the Singapore Nanopore-Expression Project (SG-NEx) which aims to systematically evaluate the use of RNA sequencing for transcriptome profiling of cancer cell-lines. We caught up with Jonathan to talk to him about his research and how long-read sequencing is changing transcriptomics.

What are your current research interests?

We are interested in all aspects of quantitative RNA biology and the technologies that allow us to study RNA in the cell. We are working on alternative promoters, splicing, RNA modifications, and computational methods that help to address our questions. Recently, Oxford Nanopore cDNA and RNA sequencing has become a major focus of my lab.

What first ignited your interest in transcriptomics?

As a postdoc, I worked on an RNA binding protein called SON which is essential for human embryonic stem cells. Most of the well-known stem-cell genes are transcription factors which regulate gene expression levels, however SON was very different as it did not act through changes in gene expression. Instead, we found that regulation at the RNA level through splicing was the key to understanding SON’s function. This project first convinced me that the transcriptome is only barely understood, and I’m still fascinated by the many questions that remain open.

How is long-read sequencing changing the study of transcriptomics? How is it benefitting your work?

Long-read RNA sequencing will enable us to quantify gene isoforms, something that is still very difficult with short-read sequencing. Direct RNA sequencing has a lot of potential as it might help to avoid some biases and allow us to identify RNA modifications. We have started several new collaborations with scientists, clinicians, and with industry who are all excited about the new possibilities using long-read sequencing.

What impact could a better understanding of the cancer transcriptome have on patients?

The cancer transcriptome is like a very high dimensional pathology report, but at the moment we still can’t fully read or interpret it. A better understanding, combined with a fast and simple profiling technology, could provide new ways to guide clinical decisions in the future.

What have been the main challenges in your research and how have you approached them?

One of the major challenges when we started using Oxford Nanopore technology was the variation in throughput. We tried many different things, but this really changed with the new flow cell and an updated kit. We now get consistent runs with sufficient depth, but we now have started to face new challenges, like what to do with the massive amount of raw sequencing data generated from the PromethION. I find it extremely useful to exchange information with other scientists working on this technology.

What’s your advice for someone getting started?

I very much recommend thinking about data analysis when designing experiments. Long-read RNA sequencing data is very rich in information, and it can be extremely helpful when computational and experimental scientists work together from the beginning. I would also recommend making use of publicly available data, such as SG-Nex. When we started, no public data was available, and every step was a challenge to learn. For computational people, I would also suggest downloading data to get experience with file formats, learn about quality control, have a reference that you can compare to your own data, and implement, run, and test pipelines.

What’s next for your research?

The SG-Nex project is Singapore’s contribution to understanding the power of long-read RNA sequencing. Our next step is to provide the complete data and comparison for all the cell lines across all the sequencing protocols, which we hope will be a very useful resource for anyone getting started, or already working with this technology. We currently test how to apply direct RNA sequencing to clinical samples, which is the next big frontier.


Jonathan Göke will be presenting ‘The SG-NEx project: nanopore long-read RNA-sequencing of human cancer cell lines’ webinar with Technology Networks on Thursday 28th February 5pm GMT/12pm EST/9am PST


Jonathan is a principal investigator at the Genome Institute of Singapore and the National Cancer Center Singapore. Jonathan's research focuses on computational transcriptomics with a particular interest in genomics technology and translational aspects in cancer. He received his PhD in Computational Biology from the Max Planck Institute for Molecular Genetics in Berlin. Jonathan has studied at Freie Universität Berlin in Germany, Sheffield University in the UK, and Stanford University in USA.