DrRory Johnson

Decoding the "Dark Matter" of the Genome in Health and Disease

The mission of the Laboratory for Genomics of Long Noncoding RNA and Disease (GOLD Lab), led by Professor Rory Johnson, is to understand the functions of the non-protein-coding genome and to turn those findings into new therapies.

Only about 2% of human DNA codes for proteins. The rest, often called the genome's "Dark Matter," was long dismissed as junk. However, the past two decades of research have shown that this is incorrect: the noncoding genome is home to numerous functional elements, in particular long noncoding RNAs (lncRNAs), and that these control processes central to health and disease. We combine high-throughput experimental methods (CRISPR-Cas9 screening, RNA sequencing) with computational biology, and we build much of our own software and methodology. Our work falls into four areas.

1. Mapping the human transcriptome

The genome cannot be understood until it is annotated. Prof. Johnson has been a member of the GENCODE Consortium since 2010, co-leading the effort to build the reference map of human lncRNAs. These annotations define where genes sit and are a standard resource for the research community. He helped develop Capture Long-Seq (CLS), which couples targeted RNA capture to long-read sequencing to map full-length lncRNA transcripts, and which underpinned much of the growth in lncRNA catalogues.

Derrien, Johnson et al. Genome Research (2012); Lagarde, Uszczynska-Ratajczak et al. Nature Genetics (2017); Uszczynska-Ratajczak et al. Nature Reviews Genetics (2018); Kaur et al. Nature Genetics (2024)

2. Tools to assign function

Having identified genes, we must work out their biological roles and mechanisms. This is particularly hard for lncRNAs because they make no protein, so standard methods cannot be applied. We build new tools to overcome this.

CRISPR-Cas9 screening: we developed DECKO, a scalable CRISPR method for deleting lncRNA genes, which lets us run high-throughput loss-of-function screens to find the lncRNAs that cells need to survive or to resist drugs. Aparicio-Prat, Arnan et al. BMC Genomics (2015)

The RIDL hypothesis: we proposed that ancient transposable elements have been domesticated to serve as functional domains within lncRNAs (Repeat Insertion Domains of LncRNAs). Carlevaro, Polidori, Das et al. Genome Research (2019); Plaisance et al. Nature Communications (2022)

Computational prediction: we design data-driven methods to infer lncRNA function and mechanism. Our pipeline TransCistor was the first to classify lncRNAs as cis- or trans-acting, and our database ElementalDB is the first comprehensive catalogue of lncRNA functional elements. Dhaka et al. Nucleic Acids Research (2024)

3. Cancer genomics: finding noncoding cancer genes

A central question for the lab is whether lncRNAs drive cancer, through altered activity or through mutation, and whether they can be turned into precision RNA therapies. Review: Coan et al. Nature Reviews Genetics (2024)

We built ExInAtor, the first software pipeline designed to find somatic driver mutations in lncRNA genes using tumour genomes. Lanzós et al. Scientific Reports (2017)

As contributing members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, we applied ExInAtor across thousands of tumour genomes to build the first comprehensive map of lncRNA driver mutations. This line of work now continues within Genomics England. Rheinbay et al. Nature (2020)

We then showed experimentally that mutations in these lncRNAs can increase the fitness of tumour cells, direct evidence that they act as cancer drivers. Esposito, Lanzós et al. Nature Communications (2023)

4. RNA therapeutics

The aim is to turn these discoveries into medicines, with a focus on non-small cell lung cancer. Once we identify a lncRNA that a tumour depends on, we can target it with antisense oligonucleotides (ASOs). We have developed potent ASOs that suppress tumour growth in preclinical models. Esposito, Polidori et al. Cell Genomics (2022)

We pursue the commercialisation of this work directly: we hold patents on RNA therapeutic agents and are working to move candidates toward the clinic.

Full list of publications here: https://scholar.google.com/citations?user=HaMHn6MAAAAJ&hl=en&oi=ao