2024
NEW PAPER: Strand-resolved mutagenicity of DNA damage and repair
12 June 2024
Our latest paper was published today in Nature!
Strand-resolved mutagenicity of DNA damage and repair
Aitken Lab members John Connelly, Claudia Arnedo-Pac, and Sarah all contributed to this collaborative project, along with friends and colleagues at MRC Human Genetics Unit, University of Edinburgh (UK), IRB Barcelona (Spain), DKFZ (Germany), EMBL-EBI (UK), and of course Cancer Research UK Cambridge Institute.
Read Sarah's tweetorial here: https://x.com/S_J_Aitken/status/1800916080418082939
And read more on the MRC Toxicology Unit website: A tale of two strands: how DNA strand asymmetry affects damage, repair and mutation rates
NEW PAPER: DNA lesion bypass and the stochastic dynamics of transcription-coupled repair
08 May 2024
Today, a new paper was published in PNAS, which is part of our wider body of work on lesion segregation and strand interactions in DNA damage and repair.
DNA lesion bypass and the stochastic dynamics of transcription-coupled repair
Read Michael's paper here: https://www.pnas.org/doi/10.1073/pnas.2403871121
And a commentary here: RNA polymerase tracking along damaged DNA: Impact on DNA repair and mutagenesis
Happy DNA day
25 April 2024
Introducing the repair squad...!
This story follows Pol the polymerase as they find some unexpected damage on the DNA they are replicating and the consequences of this damage. It is based on the research of the Aitken lab and introduces the topics of DNA duplication, DNA damage, lesion segregation and multiallelism.
Claudia Arnedo Pac and Sarah worked with artist Claudia Flandoli
to create this comic - download it here: https://drive.google.com/file/d/1DDG-P0MbPjkFP6GYt3XyBm4VUx6ZQ51V/view
Read more about the comic here: https://www.mrc-tox.cam.ac.uk/public-engagement/science-art-projects/comics
Mutations in Time and Space,
Edinburgh UK
23-25 April 2024
Sarah was selected to give a talk on "Rerunning tumour evolution reveals germline influences on mutagenesis and cancer susceptibility" and invited to take part in the panel discussion "Mutations in time and space – bridging evolutionary biology and translational cancer research" at the inaugural Mutations in Time and Space meeting (Edinburgh, UK).
NEW PAPER: Single-mitosis dissection of acute and chronic DNA mutagenesis and repair
16 April 2024
Sarah contributed to a new paper, published today in Nature Genetics, which shows mirrored lesion segregation in sister cells.
Single-mitosis dissection of acute and chronic DNA mutagenesis and repair
Read more here: https://doi.org/10.1038/s41588-024-01712-y
Fundamental Biology of Cancer meeting
Cambridge, UK
19 January 2024
Sarah was invited to give a talk at the second Fundamental Biology of Cancer meeting (Cambridge, UK).
She introduced the lab's work on "Disentangling Genome Heterogeneity".
NEW PAPER: The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma
10 January 2024
Jose and Sarah contributed to this paper, published today in Nature Cancer, in collaboration with researchers at ICR (London, UK), MD Anderson (TX, USA), the Beatson (Glasgow, UK), and others.
The artificial intelligence-based model ANORAK improves histopathological
Read more here: https://doi.org/10.1038/s43018-023-00694-w
NEW REVIEW - Cancer Evolution: A Multifaceted Affair
01 January 2024
Sarah was invited to contribute to a review article published today in Cancer Discovery. Cancer Evolution: A Multifaceted Affair
Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.
Read more here: https://doi.org/10.1158/2159-8290.CD-23-0530
2023
Happy holidays from the Aitken Lab!
31 December 2023
Celebrating the end of a very successful month (and year!) for the our team!
NEW PAPER: Hotspot propensity across mutational processes
22 December 2023
Congratulations to Dr Claudia Arnedo-Pac for her publication today in Molecular Systems Biology. This work is from her PhD with Professor Núria López-Bigas at the IRB Barcelona, Spain.
Read the paper here: Hotspot propensity across mutational processes.
NEW GRANT: Congratulations to Hashim!
20 December 2023
Congratulations to PhD student Hashim Ahmed Nur, who has been awarded a Wolfson Travel and Research Grant to attend the DNA Damage, Mutation and Cancer Gordon Research Conference next year in Ventura, California, USA.
NEW GRANT: Congratulations to Claudia and Jose
13 December 2023
Congratulations to our Postdoc, Dr Claudia Arnedo Pac, and Academic Clinical Fellow, Dr Jose Coelho Lima, who have being awarded a Postdoctoral Collaborative Grant by The Pathological Society of Great Britain & Ireland.
Best postdoc talk award for Claudia!
08 December 2023
Today was the MRC Toxicology Unit Annual Science Day, including the award ceremony. Congratulations to our postdoc, Claudia Arnedo Pac, who won the "2023 Best Postdoc Seminar Speaker" from all of this years weekly seminars!
EMBL Cancer Genomics
Heidelberg, Germany
15 November 2023
This week Claudia, Hashim, and Sarah are at EMBL Cancer Genomics in Heidelberg, Germany.
Between them they have three posters, two flash talks, a session co-chair, and a session chair!
4th Crick Cancer Conference
London, UK
08 October 2024
Today, Hashim is presenting his PhD work as a poster at the 4th Crick International Cancer Conference.
Welcome to our new PhD students - Emma and Francesca
03 October 2023
This week we welcome new PhD students to the MRC Toxicology Unit, including Emma Reilly (part of the UoC-AstraZeneca studentship programme) and Francesca Eichacker (joint with the Patil lab, on the ITTP programme).
Congratulations to DrDr Connelly!
28 August 2023
Congratulations to John Connelly who has successfully defended his PhD, and joins the double-doctor club.
John was a joint clinical PhD student with Professor Martin Taylor at MRC Human Genetics Unit, Institute for Genetics and Cancer, University of Edinburgh, as part of the ECAT Programme.
Farewell to Constantijn
21 August 2023
On Friday, Constantijn Scharlee completed his summer internship in our lab. While he was here, we introduced him to punting. Now we wish you the best of luck with your final years of medical school at KU Leuven!
EACR 2023 CONGRESS.
TURIN, ITALY
15 June 2023
Claudia and Sarah attended the EACR Congress in Turin, Italy. Claudia presented her preprint: “Mutational processes creating passenger hotspots across the genome”.
CRUK Clinician Scientist Fellowship for Sarah!
June 2023
Our group leader, Sarah, has been awarded the CRUK Clinician Scientist Fellowship! This £1.1M award will allow use to develop Genomic Pathology approaches to identify digital biomarkers in Liver Cancer.
Thank you to everyone who has supported, mentored, and collaborated to get here - you know who you are.
JOHN IS PhDone
09 June 2023
Today we are celebrating the last day of John’s PhD.John spent the final year of his PhD with us at the MRC Toxicology Unit, visiting from Prof. Martin Taylor's lab at the MRC Human Genetics Unit, University of Edinburgh. He's done some great work using computational pathology and machine learning (preprint coming soon) and will be greatly missed!
BEATSON CANCER SEMINAR SERIES,GLASGOW UK
30 March 2023
Sarah was invited to give a talk in the Glasgow Cancer Seminar Series at the Beatson Institute for Cancer Research. Really interesting discussions with computational, experimental, and clinician scientists on all things cancer research. Wonderful combination of people, science, and technologies.
CAMBRIDGE FESTIVAL
26 March 2023
This weekend we volunteered at the Cambridge Festival to engage members of the public (or all ages!) with our research. Malina, Cat, Mark and Sarah were all there. We looked at cells with a virtual microscope, made lungs with paper bags and straws, and pipetted different types of glitter...
And #HeppieTheHepatocyte was on offer at the "Tattoo my Science" event - thanks to Claudia's artwork!
NEW TEAM PHOTO
06 March 2023
We finally have an official lab photo!Left to right: Hashim Ahmed Nur, Claudia Arnedo Pac, Sarah Aitken, John Connelly, Malina Anghel.
Not pictured: Jose Coehlo-Lima, Áine McColgan
PATHSOC WINTER MEETINGLONDON, UK
02 February 2023
This week John and Sarah attended the PathSoc winter meeting at the Royal Society of Medicine: "Unleashing the edge power of pathology". John presented his PhD work "Inference of germline and somatic variation using weakly-supervised deep transfer learning". In the Jean Shanks and Pathological Society Symposium, Sarah presented "Disentangling strand interactions in DNA damage and repair". She was also invited to the National Academic Trainee Network meeting to talk about "Clinician scientists – An insight into the job".
GENOME STABILITY NETWORK MEETINGCAMBRIDGE, UK
13 January 2023
Claudia, Hashim, and Sarah attended the Genome Stability Network today. Lots of very interesting posters, talks, and discussions.
2022
SEASONS GREETING FROM AITKEN LAB
23 December 2022
Celebrating a year of building the Aitken Lab team! And we were joined by our friends from the Histopathology and Light Microscopy Core Facilities.
INTRODUCING DR ARNEDO PAC!
15 December 2022
Congratulations to Claudia, now Dr Arnedo Pac, who successfully defended her PhD thesis today at IRB Barcelona.
CONGRATULATIONS, MALINA!
12 December 2022
Congratulations to Malina Anghel, who graduated today from her Masters degree at Manchester University.
DIGITAL PATHOLOGY AND AI CONGRESS
HEATHROW, UK
07 December 2022
This week is the Digital Pathology and AI Congress!
John Connelly will talk about using Computational Pathology and Machine Learning to predict genomic features from histology images.
The MRC Toxicology Unit Histopathology Facility will present their validation of a multiplex-immunofluourescence assay for neural proteins.
SYMBLS22
CAMBRIDGE, UK
25 November 2022
Hashim Ahmed Nur presented his work today at the Symposium for Biological and Life Sciences 2022.
He presented his work on the cellular responses to platinum-based DNA damaging agents in liver cancer models.
WE ARE HIRING - PHD STUDENTSHIP
01 November 2022
We are hiring: AstraZeneca-Funded Non-Clinical PhD Studentship to join us in October 2023.
Project: Error-corrected sequencing of carcinogenic nitrosamines in a human liver spheroid model
Deadline: 05 December 2022
WELCOME MALINA!
05 October 2022
Today we welcome another new lab member! - Malina Anghel its starting her PhD with us.
Malina joins us from the University of Manchester, where she did her Masters in Tissue Engineering for Regenerative Medicine.
WELCOME CLAUDIA!
03 October 2022
We are delighted to welcome Claudia Arnedo Pac to the lab - she starts her postdoc with us today!
Claudia joins us from the Institute for Research in Biomedicine (IRB) Barcelona, where just did her PhD in Bioinformatics and Biomedicine with Prof. Núria López-Bigas in the Barcelona Biomedical Genomics (BBG) Lab.
WE ARE HIRING - POSTDOC (GENOMICS)
26 September 2022
We are hiring: Postdoctoral researcher (Research Associate) in Genome Biology or Genomics to join our team!
Deadline: 24 October 2022
RIDE ACROSS BRITAIN FOR CRUK
18 September 2022
Sarah completed her end-to-end bike ride of the UK, from Lands End to John O'Groats in September.
The final tally was: • 978 miles / 1574 kilometres • 56,931 feet climbed • 9 days • 2 wheels • 1 tent • 39 bananas • 0 punctures
Thanks to generous sponsorship from friends, family, and colleagues I reached my fundraising target for Cancer Research UK.
Any final donations are of course welcome!
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
EUROPEAN CONGRESS OF PATHOLOGY
BASEL, SWITZERLAND
07 September 2022
John Connelly and Jose Coelho-Lima both gave talks this week at the European Congress of Pathology in Basel, Switzerland.
Here is a glimpse of John's brilliant talk on "Predicting genetic variation from quantitative tissue phenotypes using explainable machine learning".
Jose presented his clinical project "Cardiac arrest with successful cardiopulmonary resuscitation induces histologic changes that correlate with survival time and lead to misdiagnosis in sudden arrhythmic death syndrome"
CAMBRIDGE BIOSCIENCES DTP SYMPOSIUM
25 July 2022
Hashim Ahmed Nur attended the Cambridge Biosciences DTP Symposium.
HELLO AND GOODBYE!
30 June 2022
Today we said goodbye to Jose Coelho-Lima, who has finished his NIHR Academic Clinical Fellowship with us, and heading back to clinical work (for now).
We also welcomed John Connelly to the lab, who is joining us from Prof. Martin Taylor's lab at our sister Unit, the MRC Human Genetics Unit in Edinburgh.
PULMONARY PATHOLOGY SOCIETY MEETING, CORK, IRELAND
27 June 2022
Jose Coelho-Lima attended the Pulmonary Pathology Society meeting in Cork.
EUROPEAN CONGRESS ON DIGITAL PATHOLOGY (ECDP). BERLIN, GERMANY
16 June 2022
John Connelly attended the European Congress on Digital Pathology in Berlin.
His work was selected for an oral presentation: "Using machine learning to infer whole genome duplication from tumour nuclear morphology".
NEW PREPRINT: STRAND-RESOLVED MUTAGENICITY OF DNA DAMAGE AND REPAIR
10 June 2022
Strand-resolved mutagenicity of DNA damage and repair
We recently discovered that some DNA lesions (damaged bases) segregate unrepaired into daughter cells for multiple generations, thereby generating combinatorial genetic diversity (Aitken et al., 2020). We have now leveraged this discovery to learn more about how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair (Anderson et al., 2022).
Read the preprint here.
Read Sarah's tweetorial here.
#StrandInteractions
EMBO CANCER EVOLUTION
RIMINI, ITALY
20 May 2022
Sarah was invited to the EMBO Workshop: The many faces of cancer evolution to present unpublished work from the LCE Consortium "Disentangling strand interactions in DNA damage and repair".
#StrandInteractions
IRB BARCELONA, INVITED SEMINAR
27 April 2022
Sarah was invited to deliver the IRB Barcelona Research Seminar for the Computational Biology and Preclinical Models of Cancer research nodes.
"Disentangling strand interactions in DNA damage and repair"
WE ARE HIRING: COMPUTATIONAL POSTDOC
14 April 2022
We are hiring: Postdoctoral researcher (Research Associate) in Computational Biology or Bioinformatics to join us summer/autumn 2022.
Deadline: 28 April 2022
CONTRA CONFERENCE, ANDERMATT
12 April 2022
Sarah was invited to present at the Computational Oncology Conference organised by CONTRA (Computational ONcology TRaining Alliance Innovative Training Network).
"Re-running cancer evolution in vivo to disentangle DNA damage and repair"
First in-person conference since the pre-COVID era. Enthusiastic and engaged participants. And great snow...
MEDICAL MASTERCLASSES
07 April 2022
During the Cambridge Festival 2022, two of our lab members were invited by the Department of Pathology to give Medical Masterclasses aimed at Year 12 pupils from all backgrounds interested in medicine (not just at Cambridge), followed by a Q&A with current medical students.
Jose Coelho-Lima, our Academic Clinical Fellow, discussed the role of artificial intelligence in medicine and clinical research.
And Sarah talked about "Putting pathology under the microscope".
FIRST YEAR PHD TALKS
23 March 2022
Hashim, and all of the other first year PhD students at the MRC Toxicology Unit presented an overview of their project to the other students and group leaders. Well done!
LANDS END TO JOHN O'GROATS FOR CRUK
20 February 2022
Sarah is cycling from Lands End to John O'Groats in September
• 970miles • 1552km • 9 days • 2 wheels • 1 tent •
Although I am a daily, all-weather cyclist, this will be a massive challenge - so I've signed up via Cancer Research UK to give something back for the generous support that I have received from them over the years, and I would be massively grateful for any sponsorship and for generally helping to spread the word:
https://www.justgiving.com/fundraising/SJA-LEJOG-2022
Please remember to add Gift Aid if you are eligible - thank you!
I also have another page for the Red Cross to show solidarity with the people of Ukraine and other countries who need humanitarian aid and support from the Disasters Emergency Committee.
LIVER CANCER EVOLUTION CONSORTIUM (HYBRID) MEETING
01 February 2022
This week we hosted the Liver Cancer Evolution Consortium meeting at the MRC Toxicology Unit. A truly hybrid meeting, with attendees from Edinburgh, Barcelona, Heidelberg, Hinxton, and Cambridge.
AND THEN THERE WERE FOUR!
12 January 2022
This week Hashim and Jose both joined our team.
L to R: (me), Hashim, Jose, and John.
Hashim Ahmed Nur is a MRC PhD student working on molecular and genomic responses to DNA damaging agents.
Jose Coehlo-Lima is a postdoctoral NIHR Academic Clinical Fellow, working on computational analysis of clinical histology images of lung cancers.
John Connelly is a Wellcome Trust Clinical PhD Student (University of Edinburgh). He is using machine learning to detect mutational processes in digitised pathology images of liver tumours.
2021
CAMBRIDGE HEPATOLOGY RESEARCH SEMINAR
14 December 2021
Sarah was invited to present our work on Lesion Segregation at the monthly Eastern Liver Network Cambridge Hepatology Research Seminar.
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EMBL CANCER GENOMICS
22 November 2021
Sarah presented the next instalment from the Liver Cancer Evolution Consortium at EMBL Cancer Genomics: "Re-running cancer evolution in vivo: a high-resolution multi-omics approach"
WE ARE HIRING: PHD STUDENT
16 November 2021
We are hiring: Phd studentship to join us in October 2022.
Characterisation of 3D liver models for discovery toxicology and pathology
Deadline: 02 December 2021
CRUK CAMBRIDGE INSTITUTE RETREAT
22 October 2021
Sarah was invited to present our work on Lesion Segregation at the CRUK Cambridge Institute annual retreat.
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WE ARE HIRING: PHD STUDENT
16 September 2021
We are hiring: Phd studentship to join us in January 2022.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 27 September 2021
AITKEN LAB: DAY ONE
01 September 2021
First day at the Medical Research Council Toxicology Unit in the School of Biological Sciences at the University of Cambridge.
WE ARE HIRING: PHD STUDENT
04 June 2021
We are hiring: Phd studentship to join us in October 2021.
Molecular and genomic responses to DNA damaging agents in the context of liver toxicity and disease
Deadline: 18 June 2021
WE ARE MOVING TO THE MRC TOXICOLOGY UNIT, UNIVERSITY OF CAMBRIDGE
02 June 2021
The Aitken Lab will open at the MRC Toxicology Unit, University of Cambridge in autumn 2021.
