News and events

News at the BCGB

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MRes in Functional Genome Biology starting in September 2022

BCGB and The Institute of Cancer and Genomic Sciences are launching a new MRes in functional genome biology course in September 2022. Genome biology is the biological science of the 21st century and has the potential to transform medicine. It is powerfully informative about how DNA and genomes are organised and controlled. An understanding of its core principles and how it responds to stresses and interventions is a requirement for future research leaders.

This programme places you at the centre of world-leading expertise to provide a unique training experience, offering cutting-edge taught and research training in all aspects of genome biology. As a research Masters degree, it prepares you for the next stage in a research career. Its delivery focuses on substantial hands-on, real world training to give you the employability skills you will need for PhD and industry positions.

Apply here to join this course

Post-lockdown report from BCGB (September 2021)

The last year and a half has been difficult for everyone, and especially hard for research labs that had to endure complete laboratory shut-downs for many months and severely restricted access to labs and offices at other times. However, that does not mean we have been unproductive. While working from home many of our members used this time to publish research articles based on data that they had already accumulated before the COVID19 pandemic struck. This made a substantial contribution to the University of Birmingham’s REF submission with many of these outputs ranked internally as 4 star publications. It is impossible to list them all here but here are just some of the highlights:

In the area of Epigenetics and Gene Regulation, the Bonifer/Cockerill group had a string of papers covering both Cancer Genomics and Molecular Immunology. Continuing on the theme of gene regulation and epigenetics in acute myeloid leukaemia (AML), which produced a Nature Genetics paper on gene regulatory networks in AML in 2019, Potluri et al showed in Cell Reports in 2021 that the transcription factor WT1 mediates oncogenic signalling to control AML growth. In a study in 2020, Chin et showed in Experimental Hematology that RUNX1/ETO and mutant KIT collaborate to re-programme  transcription in AML with t(8;21) translocations, while Nafria et al showed in 2020 in Cell Reports that RUNX1-ETO interferes with normal RUNX1 binding to block early myeloid cell development. Kellaway et al showed in Haematologica in 2021 that RUNX1-EVI1 disrupts the gene regulatory networks controlling differentiation in AML with t(3;21) translocations, and also showed in Life Science Alliance in 2021 that different mutant RUNX1 oncoproteins re-program different differentiation pathways. Daniel Coleman’s contribution to the Nature Genetics paper was also acknowledged when he was awarded a Goldman Fellowship in 2021 by Leukaemia UK.

On the T cell front, Bevington et al published 3 landmark papers on gene regulation and epigenetics during T cell differentiation. One study in EMBO in 2020 revealed that T cell differentiation is actually initiated by IL-2 and IL-7 when naïve T cells are activated the first time, making cells receptive to differentiation factors which are only expressed much later. A collaboration with David Wraith in Cell Reports in 2020 defined the molecular basis of a peptide de-sensitisation therapy used in Multiple Sclerosis patients that renders auto-immune cells tolerant. A collaboration with David Withers in Frontiers in Immunology in 2021 defined the molecular basis of immunological memory by using antigen-specific T cells to show that memory T cells acquire stable epigenetic priming at immune response genes in response to antigen.    

Also in the field of gene regulation in leukaemia, the Stankovic lab made major advances in the field of chronic lymphocytic leukemia (CLL). Kwok et published in Blood in 2020 the molecular basis for spontaneous regression in CLL. Marwon Kwok’s contribution was recognised with the Hamblin prize for the best CLL paper in 2020, the Trainee prize from the Royal College of Pathologists, and a 3 year fellowship from CRUK to study at Harvard.

With a change of subject now to zebrafish, the Mueller lab showed in Developmental Cell in 2021 that the germ plasm determining factor Tdrd7 controls the development of the germ plasm from primordial germ cells by programming transcriptional networks that govern cell fate decisions between germ cells and somatic cells. In a second study in Nature Communications in 2020, Nepal et al showed that many gene promoters in zebrafish, and also humans, utilise 2 distinct classes of transcription initiation sequences within individual promoters that are differentially regulated during the transition from maternal to zygotic gene expression during embryogenesis. Also in zebrafish, Rui Monteiro showed in Communications Biology that a conserved enhancer controlling the GATA2 gene is required for development of both blood cells and endothelial cells.

In one of 2 significant publications involving insect models, the Badenhorst group used drosophila as a model of inflammation to publish a study in Life Science Alliance in 2020 to show that oxidised dietary unsaturated fatty acids activate pro-inflammatory signalling pathways linked to JNK that phosphorylate the transcription factor FOXO, a transducer of insulin signalling, and render it unresponsive to insulin signalling.

In a study looking at honey bees, a study from the Soller group in Scientific Reports in 2021 revealed that the devastating effects of widely used neonicotinoid insecticides can be linked to changes in gene expression and increased susceptibility to bacterial infections.

A study of bacterial gene transcription published by the Grainger lab in Nature Microbiology in 2021 identified an abundant class of symmetrical bidirectional promoters that regulate divergent genes in E.Coli and in Archaea.

In the area of DNA replication and repair, the Stewart lab showed in Nature Communications in 2020 that the balance between early and late DNA replication is controlled by DONSON and FANCM associating with different replication origins. On a similar theme, the Akerman lab showed in Nature Communications in 2020 that different cell types share a core of replication origins that are defined as G-rich origins. In another study in The Journal of Clinical Investigation from the Stewart and Higgs labs in 2020, they showed that germline mutations in the RBBP8 gene, a regulator of homologous recombination during DNA repair, are responsible for a subset of early onset breast cancers. A study from the Saponaro lab showed in Cell Reports in 2021 that persistent transcription during DNA replication leads to a delay of replication timing of these transcribed regions. A team effort from several groups in BCGB, led by Paloma Garcia and published in EMBO Reports in 2021, showed that MYBL2 functions to suppress replication stress and genome instability in stem cells. A study from the Petermann and Morris labs in Nature Communications in 2020 identified the priming polymerase PrimPol as factor that leaves gaps in replicated DNA where replication is stalled by bulky DNA adducts, which require post-replication repair via DNA resection by RAD51 and homologous recombination.

Finally on the COVID19 front, Pawel Grzechnik joined a team of UoB chemists and virologists to develop molecules that form supramolecular barrel structures capable of blocking viral replication. The characterisation of these novel therapeutics was published in 2021 in Angew Chem Int Ed Engl.

Promotions and awards for BCGB members in 2020 and 2021

Jo Parish and Andrew Beggs were promoted to Professor. 
Eva Petermann and Aga Gambus were promoted to Reader.
Dr Martin Higgs, Dr Marco Saponaro, and Dr Ildem Akerman were promoted to Senior Lecturer.

Well done to all. 

 

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Jo Parish

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Andrew Beggs

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Eva Petermann

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Aga Gambus

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Martin Higgs

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Dr Marco Saponaro

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Dr Ildem Akerman

Previous news 

In 2019, Professor Jo Morris published a paper in Nature describing a novel mechanism regulating the structure of the BRCA1 protein and how mutations in breast cancer prevent the BRCA1 protein from adopting the correct structure. BRCA1 normally protects the genome from DNA damage and this function is controlled by an isomerase that puts a bend in the BRCA1 protein. The Morris laboratory showed that some mutations occur in the isomerisation site and bypass this mode of regulation, and block normal BRCA1 function. 

 

Photo of Jo Morris
 
Professor Jo Morris
 

 

 

 

Promotions and awards for BCGB members in 2019

Dr Jo Parish and Claire Davies were both promoted to reader, in recognition of their outstanding progress as rising stars in research. Clare was recently awarded £1.4 million by the CRUK to study arginine methylation in cancer, based on high profile publications in Molecular Cell and Cell Reports, while Jo was awarded a MRC grant to study HPV based on her long term research and extensive publications in the area of viral gene regulation and replication.

Clare Davis Landing Page promo row

 

Dr Clare Davies

 

 

 

Dr Jo ParishJo Parish

 

 

 

 

 

Continuing outstanding grant success

The strong recent track record of BCGB members at winning major grant funding has continued with the award of ~ £10 million in grant funding in the first few months of 2019.

These awards include

  • £4 million for 3 CRUK programme grants for Eva Petermann, Jo Morris and Tanja Stankovic
  • £3.4 million for 2 Wellcome Trust grants for Ian Tomlinson and Aga Gambus
  • Research Council Project grants for Dr Marco Saponano, Dr Eva Petermann, Dr Sheela Jayaraman, and for Professor Conny Bonifer together with Professor Peter Cockerill. 

 

New drug targets identified for personalised medicine in acute myeloid leukaemia

Peter Cockerill and Constanze Bonifer

The group of Constanze Bonifer and Peter Cockerill have revealed the roles that different types of gene mutations play in causing acute myeloid leukaemia in a study that was the culmination of a decade’s research. The findings of the team mean that doctors are now one step closer to being able to provide tailored and targeted treatment specific to individual AML patients. By identifying the specific mutations present in each AML patient and gathering genome-wide data on each of them, they were able to identify the main trigger points where critical mutations feed through to other genes that control the cells’ identity and behaviour.

Crucially, AML cells from patients with the same types of mutations always show the same pattern of abnormal gene regulation when they become cancer cells. This means that personalised medicine will one day become a reality for AML patients, allowing a different drug to be given to treat each form of AML. This has already been validated for one common subtype in AML.

In collaboration with Professor Olaf Heidenreich’s team at Newcastle University, this team also found that a growth-promoting gene, called CCND2, was crucial for the survival of AML with t(8;21) translocations. The already approved breast cancer drug called palbociclib designed to inhibit CCDN2 was able to block AML tumour development - therefore identifying it as a drug that could be used to target and treat AML.

These results were just published in

Assi et al (2018). ‘Subtype-specific regulatory network rewiring in acute myeloid leukemia’. Nature Genetics. DOI: 10.1038/s41588-018-0270-1

Martinez-Soria et al. ‘The oncogenic transcription factor RUNX1/ETO corrupts cell cycle regulation to drive leukaemia transformation.’  Cancer Cell. DOI: 10.1016/j.ccell.2018.08.015

2019 BCGB away day trip to the Malvern Hills

This year we had our most ambitious BCGB away yet, with a hike up to the top of the Worcestershire Beacon, the highest point in the Malvern Hills. The biggest challenge of the trip was not the 200 m climb, but the weather. Luckily we missed the worst of the torrential rain that had been falling all day as we all headed down to Malvern on the train. Once on the walk we took shelter at St Anne’s well (pictured) until the rain stopped, and the mist lifted as we hiked to the top with views all around. We arrived at the top in atmospheric conditions with mist swirling all around, before walking back down to a dinner together in Malvern. 

Group on the 2019 BCGB Away Day

St Anne’s Well, Malvern (June 2019) 

2019 BCGB Away Day group reaching the highest point in the Malvern Hills 2019

Worcestershire Beacon, the highest point in the Malvern Hills (June 2019)

 

2018 BCGB Away Day visit to Packwood House

2018 BCGB group on their Away Day

The 2018 BCGB away day in the Warwickshire countryside was a great day out with over 40 of our members taking part. We started out in Lapworth with a walk along the Stratford Canal to the Elizabethan manor at the National Trust property at Packwood House, and finished with a dinner overlooking the Grand Union Canal.

2017 BCGB Away Day visit to Soho House

This event explored the industrial roots of Birmingham as the “Workshop of the World”. It began at Galton Bridge (built by Telford) and followed the route of the Birmingham Canal (built by Brindley). It included a visit to Soho House, the home of the 18th century industrialist Matthew Boulton. Soho house was famously the meeting place for the Lunar Society, a group that included James Watt, Erasmus Darwin, Josiah Wedgewood and Joseph Priestley, which met once a month to discuss science and philosophy.

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2016 BCGB Away Day Walk in the Woods

Members of the BCGB enjoyed a walk in the Lickey Hills for their 2016 away day at Barnt Green.

2016 BCGB away day IMG_6825

2015 BCGB Bluebell Woods Walk

Pictured are members of BCGB who went on the walk through the bluebells in the Lickey Hills (May 2015) 

2015 bluebell walk

Seminars at the BCGB

BCGB internal meeting

Summer 2019 speakers (PI)

Wednesday 17th July Onofrio Zanin (P. Grzechnik) 

The role of the 5’ cap structure in the transcriptional cycle

All meetings at 09.30 in IBR N143

Visiting seminar speakers

2019

29 January - Phillip Voigt (University of Edinburgh)

26 February - Duncan Sproul (University of Edinburgh)

26 March - Douglas Vernimmen (University of Edinburgh)

22 October - Majolein Vansluis (National University of Ireland, Galway)

26 November - Ester Hammond (University of Oxford)

10 December - Doug Higgs (Weatherall Institute of Molecular Medicine, University of Oxford)


Previous visiting seminar speakers

2018

23 January - Lynne Cox (University of Oxford)

20 March - Richard Festenstein (Imperial Collage London)  

17 April - Panagia Filippakopoulos (SGC,University of Oxford)

22 May - Rob Klose (University of Oxford)

20 November - Delphine Larrieu (University of Cambridge)

2017 BCGB Seminar series 

21 February - Dr Veronique Azuara (Faculty of Medicine, Imperial College, London)

21 March - Dr Cristina Lo Celso (Francis Crick Institute, London)

25 April - Dr Petra Hajkova (MRC Clinical Science Centre, Imperial College, London)

9 May - Dr Chiara Francavilla (Faculty of Life Science, University of Manchester)

13 June - Professor Adam Mead (Radcliffe Department of Medicine, University of Oxford)

26 September - Narvaez (Astra Zeneca)

21 November - Andrew Jackson (University of Edinburgh)

5 December - Duncan Odem (Cancer Research UK  Cambridge Institute)

2016

19 January - Florian Grebian (Ludwig Boltxmann Institute for Cancer Research), "Identification of critical effectors of C/EBPalpha mutant AML". 

16 February - Professor Elias Campo (Research Director, Hospital Clinic, Barcelona), “Clinical impact of recurrent coding and non-coding mutations in CLL”.

19 February -  Professor Daniel G. Tenen (Director of the Blood Program of the Harvard Stem Cell Institute, Director of the Cancer Science Institute of Singapore), “Epigenetic regulation by RNA in a normal and malignant context”. 

15 March - Professor Dean Jackson (University of Manchester), “Activation of signalling through the NF-kappaB and p53 stress response networks: mapping signalling oscillations to cell fate".

19 April - Dr Adele Murrell (University of Bath), “Models for studying epigenetic gene regulation in breast cancer”. 

24 May - Professpr Claus Nerlov (University of Oxford), “Dissecting hematopoietic stem- and progenitor cell populations using molecular and functional single cell approaches”.

20 September - Professor Tom Owen-Hughes (University of Dundee), “Structural and genomic insights into chromatin organisation”.

21 September - Dr David Blakey (Mina Therapeutics), “Pioneering small activating RNA oligonucleotides for transcriptional activation: Preclinical studies on MTL-CEBPA 

29 November -  Dr Sarah McClelland (Barts Cancer Institute, London)

13 December - Dr Nathalia Gromak (Sir William Dunn School of Pathology, Oxford)

2015

25 February -  Francis Stewart (University of Dresden), "Regulation of the Genome by MLL Family Histone Methyl Transferases".

17 March -  Peter Fraser (Babraham Institute),"3D Structure and Function of the Genome: from Cell Populations to Single Cell Analyses". 

21 April - Marco Saponaro (Francis Crick Institute), "Transcription Regulation in the Context of Genome Stability Maintenance". 

19 May - Bertie Gottgens (University of Cambridge), "Single Cell Biology Links Cellular Function with Molecular Profile to Reveal Gene Regulatory Networks". 

16 June - Paola Scaffidi, "Epigenetics and functional intra-tumour heterogeneity".

25 June - Professor Ann Harris (Northwestern University, Chicago), "Coordinating epithelial function: from single locus to transcriptional network".

8 September - Dirk Schübeler (Friedrich Miescher Institute for Biomedical Research, Basel), "Reading and writing DNA methylation".

8 September - Asifa Akhtar (Max Planck Institute of Immunology and Epigenetics, Freiburg). "Epigenetic regulation by MOF containing complexes".

23 October -  John Bushweller (University of Virginia), "Drugging the undruggable – Targeting transcription factors for cancer therapy".

24 November -  Dr Marco Saponaro (Institute of Cancer and Genomic Sciences),  Transcription regulation in the context of genome stability maintenance”.

1 December -  Dr Tatjana Sauka-Spengler, Associate Professor of Genome Biology, MRC Senior Research Fellow, University of Oxford “Pioneering the chromatin for neural crest specification”.