Programme Publications

CRISPRcleanR opens new ways for discovering novel cancer drug targets, by correcting CRISPR-Cas9 drop-out screens

17 August 2018

CRISPR-Cas9 is a powerful technology with important applications in cancer research, as it can help identify genes that are essential for cancers to grow. However, cancer cells can accumulate extra copies of specific genes, which are then wrongly classed as being essential for cancer. Researchers from the Wellcome Sanger Institute have created a new computational tool, called CRISPRcleanR, that accounts for this undesired bias in the data derived from CRISPR-Cas9 screens.

Published in BMC Genomics and as part of the Cancer DepMap at the Wellcome Sanger Institute, the method allows better interpretation and prioritising of gene hits for the development of new anti-cancer therapies. Notably, this approach does not require any information about the number of extra gene copies. The method will improve the analysis of CRISPR-Cas9 knockout screens to identify essential cancer genes.

Exploring the role of stromal osmoregulation in cancer and disease using executable modelling

7 August 2018

Researchers at the MRC Cancer Unit have shown how a set of proteins can change cancer cell behaviour. Using computer simulations, they discovered how coordination between a network of membrane transporters can be exploited to improve existing drug action, and potentially generate new treatments. These transporters are used to maintain the balance of chemicals inside and outside the cell. The gradients of these chemicals are then used in processes like cell size maintenance, and control fundamental behaviours such as cell movement and growth.

In their new publication, researchers from Dr Ben Hall’s group show for the first time that alterations in the expression of these membrane transporters consistently occurs in all cancers. Going further, the researchers were able to construct a computational model of the key chemical gradients and transporters within a cell, and show precisely how changes in the expression of them can alter cancer cell behaviour. This research is a start at understanding how these proteins can be used as potential markers or drug targets in the future.

A novel Atg5-shRNA mouse model enables temporal control of Autophagy in vivo

23 July 2018

Autophagy is a process of cellular self-digestion that is required to prevent the build-up of damaged molecules that would otherwise predispose to a range of diseases including neurodegeneration and cancer. In their new publication, researchers from Dr Masashi Narita’s Group at the CRUK Cambridge Institute, and their collaborators, describe a new model in which we can control when and where autophagy happens. Instead of completely deleting a gene, they developed a system that allows us to turn off and on a key autophagy gene, blocking and re-establishing autophagy, respectively. This has enabled them to perform experiments that were previously impossible and uncover novel insights. In one example, the researchers were able to show that autophagy inhibition can drive liver damage, yet liver fibrosis occurred only after autophagy restoration. Such models are necessary to test the role of autophagy at different stages of disease, such as in cancer where it may have different roles in tumour initiation, progression, and treatments.

Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells

20 July 2018

Breast cancer is the most common cancer in the UK, with up to 10% of hereditary cases due to inheriting a faulty cancer-causing gene, for example, mutations in the BRCA1 gene. Individuals with BRCA1 mutations are at high risk of developing breast cancer, and often opt for prophylactic breast removal, as was reported for Hollywood actress Angelina Jolie. Previous research in Professor Steve Jackson’s Group at the Gurdon Institute led to the development of PARP inhibitors, a new class of cancer therapy which is highly effective in treating cancers with these mutations. Unfortunately, drug resistance is a common response, and so his group set out to establish how this resistance might develop.

Using state-of-the-art CRISPR gene editing technology, the researchers scanned the human genome for factors which, when mutated, could cause drug resistance in cells that lacked BRCA1. One of these factors was the previously uncharacterised Shieldin complex.

BRCA1 is critical for performing the accurate type of DNA repair known as homologous recombination (HR). This is counterbalanced by an opposing ‘error-prone’ repair pathway known as non-homologous end-joining (NHEJ). The researchers identified Shieldin as a new component of the NHEJ pathway. BRCA1-negative cells rely on this error-prone DNA repair pathway, which makes them susceptible to PARP inhibitors. If Shieldin is removed from these cells, the imbalance between the repair pathways is reversed, restoring the ability of the cell to perform DNA repair by HR, overcoming the toxicity of PARP inhibitors and therefore leading to drug resistance. The study went on to show that resistance to PARP inhibitors can lead the same cancer cells to develop vulnerabilities to alternative cancer treatments, such as radiotherapy or platinum-based chemotherapy.

Inhibition of the acetyltransferase NAT10 normalizes progeric and aging cells by rebalancing the Transportin-1 nuclear import pathway

11 July 2018

One crucial part of human cells is a structure called the nuclear envelope, which surrounds the cell nucleus – home to our DNA. This structure is essential for maintaining normal nuclear architecture and cell function. Dysfunction of the nuclear envelope leads to various human diseases, including the rare, but devastating Hutchinson-Gilford progeria syndrome (HGPS) for which there is no current cure. In their new publication, Professor Steve Jackson’s Group at the Wellcome Trust Gurdon Institute and Dr Delphine Larrieu’s Group at the Cambridge Institute for Medical Research identified a new pathway – the Transportin-1 pathway responsible for importing several proteins into the nucleus – as being affected in HGPS. These proteins are involved in important cellular processes including organisation of DNA structure and regulation of gene expression. Consequently, in HGPS, they cannot effectively reach the nucleus and are therefore unable to play their normal roles. The authors show that by targeting a protein called NAT10, we can restore the Transportin-1 pathway in HGPS cells, leading to improvement of DNA structure, gene expression re-balancing, and delayed entry of cells into senescence.

The evolutionary history of dogs in the Americas

9 July 2018

Transmissible cancers are clonal cell lineages that can spread between individuals via transfer of living cancer cells. One of the oldest known contagious cancers is Canine Transmissible Venereal Tumour (CTVT). CTVT is usually sexually-transmitted between dogs and manifests as genital tumours. This dogged disease first arose from the cells of an early domesticated dog thousands of years ago and has since then "metastasized" through global dog populations. In their new study, Dr Elizabeth Murchison’s Group at the Department of Veterinary Medicine trace the historic origin of this cancer lineage using samples of DNA from ancient canids. The study reveals that CTVT first arose over eight thousand years ago in a “founder” individual very closely related to an extinct population of dogs that were once widespread across the Americas.

SLAM-ITseq: Sequencing cell type-specific transcriptomes without cell sorting

4 July 2018

Our body consists of various organs, which are further composed of tissues that each include diverse populations of highly specialised cells. As such, it is important to precisely look at how each cell regulates its genes in order to understand animal physiology. All the existing methods to study cell-specific gene expression require cellular or molecular sorting. This can be quite time-intensive, however, and has considerable detrimental effects on cells, leading to limited applications. Professor Eric Miska’s Group at the Wellcome Trust Gurdon Institute have developed a new method, SLAM-ITseq, which enables scientists to study gene expression in a cell-specific manner through RNA labelling combined with a novel high-throughput sequencing method. Since SLAM-ITseq eliminates the need for cellular or molecular sorting, this method can be employed to study wider cell types in an animal in an easier, yet more accurate manner than ever before.

Mutational landscape of a chemically-induced mouse model of liver cancer

28 June 2018

One cause of cancer can be exposure to chemical carcinogens. Often we think of tobacco smoke, but widely-used preservatives in bacon can be broken down by the liver into a carcinogen called nitrosamine, which may contribute to cancers in the digestive track. In their new paper, Dr Duncan Odom's Group at the CRUK Cambridge Institute used a cohort of mice to characterise what kinds of mutations occur in liver cells after exposure to a closely related compound called diethyl nitrosamine (DEN). DEN has long been used to create liver tumours, and their study applied very recently developed high throughput sequencing technologies to look at how protein coding genes can be altered in both early and later stages of tumour development. Together, the authors revealed the precise locations on a handful of cancer genes that drive tumour development, as well as the overall molecular pathways affected in a widely used model for chemically induced liver cancer.

The mitochondrial network of a U2OS cell
Constitutive regulation of mitochondrial morphology by Aurora A kinase depends on a predicted cryptic targeting sequence at the N-terminus

13 June 2018

Aurora kinase A is regarded as a promising therapeutic target in cancers, but there is still much to discover about its roles in the cell, and how these contribute to cancer progression. A new study from Dr Rhys Grant et al. in Dr Catherine Lindon's Group at the Department of Pharmacology, University of Cambridge, shows that one of these roles concerns the organization of the mitochondrial network, the energy factory of the cell, which in the presence of excess Aurora A fragments into smaller units that are thought to function less efficiently. Fragmented mitochondria are a hallmark of cancerous cells, whose metabolism is less reliant on mitochondria than healthy cells. The finding that Aurora A is targeted to mitochondria raises exciting new questions about this key player that extend beyond its well-described role in controlling cell division to a more generalized role in cytoplasmic organization and metabolism.