Research

There is evidence that cancers can originate from adult stem cells, cells which are present in all our tissues, and are necessary as they regenerate organs following cellular and tissue damage. Adult stem cells, just like embryonic stem cells, have the ability to self-renew (meaning that daughter cells will be clones of the mother cells) or differentiate (give rise to mature cells). Currently, the understanding is that these cells randomly accumulate mutations as we age which will eventually give rise to cancer cells. Generally, this process is a black box and the hope is that future research will bring more clarity to understand how most cancers happen in humans.

We are particularly interested in cellular (re)programming and epigenetics and how these processes can give rise to a large palette of cell identities as well as cancer cells. Epigenetic mechanisms (including DNA methylation, histone modifications and nucleosome positioning) allow genetically identical cells to functionally diversify and, whilst reversible, they are specific for each cell type and have essential roles in reinforcing cellular identity.

Cancer has been associated with epigenetic aberrations (since the 70s) but so far it has been difficult and cumbersome to test whether they undoubtedly alter cellular identity. Recent technological developments allowed researchers to ask this question and untangle epigenetic mechanisms that happen at many loci in the genome. We recently demonstrated, using epigenetic editing with CRISPR technology, that controlled deposition of DNA methylation at the promoter of the tumour suppressor gene CDKN2A allowed primary human cells to successfully bypass senescence (Saunderson et al., Nature Comms 2017 ). These primary cells were obtained from our institute’s tissue bank, from healthy women who have undergone breast reduction mammoplasty. Normally, these cells when cultured in vitro die due to senescence. This was prevented with the help of epigenetics. The implication of this finding is that epigenetic changes can confer selective advantage during cancer evolution and, once deposited, it will be propagated for the benefit of the cancer cell.

One of our ongoing projects aims to identify how such increases in DNA methylation could happen in cells naturally or associated with cancer. Epigenetic analysis of human cancers has revealed widespread promoter hypermethylation alongside global loss of this modification. We are using embryonic stem cells as a model system to elucidate the mechanisms of both processes. Our lab is also interested in the epigenetic changes following overexpression or mutation of a known oncogene. We seek to link signalling processes to epigenetic mechanisms and prevent downstream consequences aiding cancer evolution.

Other Activities

• Member of Biochemical Society
• QMUL Centre for Epigenetics Co-lead
• Associate editor NAR Cancer
• Mentoring young researchers to excellence
  Invited to speak at the ICR/Wellcome Trust Sanger Institute “Pathway to Independence; Developing future scientific leaders” programme (March 1st 2016, The Royal Institution of Great Britain)
• Contribute regularly to the Max Planck Institute/Göttingen University MSc/PhD Programme Alumni magazine, the latest article detailing personal experiences in my transition to academic independence, Title: "Living the dream I never dared to have" (Page 18)
• Public engagement
  Presentation at the Pint of Science Festival, London 2014 “Will a bad memory kill you: Epigenetics at a glance”, and “Genetic Puppetry” in 2016
• Invited speaker at TEDx Bucharest on “Epigenetics and Stem cells”, 16th October 2009

Major Funding

• 2024-2029 – Targeted Transformational Funding from Barts Charity “Cell-Free Epigenomics for Disease Biomarker Discovery” co-PI with Dr Branco/Dr Bell (£3,000,000)
• 2024-2028 – CRUK CoL PhD studentship “Epigenetic regulation of the immune cells, clonal hematopoiesis and cancer initiation” (£92,000)
• 2024-2025 – CRUK CoL Development Grant: “Understanding how the epigenome in blood stem cells induces an inflammatory environment” (£25,000)
• 2023-2026 – Barts Charity Large Project Grant “The tumour suppressive nature of the chromatin landscape during tissue regeneration” (£328,000)
• 2021-2024 – Barry Reed Cancer Fund PhD studentship “Why do healthy cells become cancerous?  Elucidating the origin of pre-cancerous cells” (£78,000)
• 2015-2019 – Medical Research Council, New Investigator Award, “Elucidating the molecular and epigenetic basis of cancer initiation” (£860,000)

Recent Publications

A Novel Approach: Nanopore Sequencing of Native Cell-Free DNA in Diffuse-Large B-Cell Lymphoma Patients Erblich T, Sauer C, Muyas F et al. Blood (2023) 142(10) 7170

Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation Cheng KCL, Frost JM, Sánchez-Luque FJ et al. Epigenetics & Chromatin 16(10) 39

CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny Saunderson EA, Encabo HH, Devis J et al. Proceedings of the National Academy of Sciences of the United States of America (2023) 120(10) e2300224120

Identification of mammalian transcription factors that bind to inaccessible chromatin Pop RT, Pisante A, Nagy D et al. Nucleic Acids Research (2023) 51(10) 8480-8495

Low HER2 enables dedifferentiation and transformation of normal breast epithelial cells via chromatin opening Hayat A, Carter EP, King HW et al. Disease Models & Mechanisms (2023) 16(10) dmm049894

Corrupted devolution: How normal cells are reborn as cancer precursors Lord A, Ficz G The International Journal of Biochemistry & Cell Biology (2022) 149(10) 106263

P1411: DUAL EPIGENETIC AND GENETIC EDITING OF PRIMARY HUMAN HAEMATOPOIETIC STEM AND PROGENITOR CELLS Saunderson E, Encabo H, Rouault‐Pierre K et al. HemaSphere 6(10) 1295-1296

A comprehensive approach for genome-wide efficiency profiling of DNA modifying enzymes Kyriakopoulos C, Nordström K, Kramer PL et al. Cell Reports Methods (2022) 2(10) 100187

An shRNA kinase screen identifies regulators of UHRF1 stability and activity in mouse embryonic stem cells Rushton MD, Saunderson EA, Patani H et al. Epigenetics (2022) 17(10) 1590-1607

Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle Halsall JA, Andrews S, Krueger F et al. Scientific Reports 11(10) 3009

Team

• Alice Lord
• Leo Dudley
• Lynette Graver
• Bita Arjomandi

Biography

I started my research career at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany as a masters student at the first International MSc/PhD Research School in Molecular Biology. Here I had the opportunity to work with exceptional people in various research areas and this inspired me in my work for the years to come.

I came across Epigeneticsearly on and was fascinated by the paradigms and the questions at that time, so in 2002 I decided to do my PhD with Donna Arndt-Jovin working on the Polycomb-group of genes (PcG), which control body patterning in the fruit fly model system. I found that the PcG proteins are extremely dynamic on the genes they control, presumably having the ability to quickly respond to environmental signals in development.

Later on, for my postdoctoral research, I joined the group of Prof. Wolf Reik at the Babraham Institute, University of Cambridge, in 2005 where I worked on Epigenetic reprogramming in the mammalian system. We were seeking to find the elusive mechanism capable of erasing the epigenetic memory in cells. This memory, in the form of a chemical methyl group on the 5’ position of cytosines in the DNA, is essential for normal mammalian development and for maintaining identity of adult cells. Such reprogramming happens at fertilization and in germ cells in order to re-establish totipotency in early embryogenesis. After the discovery of the TET (ten-eleven translocation) protein activity, which oxidises 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), we mapped for the first time the genomic positions where 5hmC is generated in mouse embryonic stem cells and found that indeed this mechanism is in part responsible for removing the repressive 5mC signal in DNA.

In 2013 my research indicated that epigenetic reprogramming is mediated as well by signalling networks, which control the genes involved in maintaining the methylation patterns in cells. This made me understand the relevance of such mechanisms in health and disease therefore I decided to investigate them in adult stem cells which regenerate our body and have direct impact on ageing and cancer. I was appointed Lecturer and Early Career Researcher in September 2013.