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SCIENTIFIC REPORT 2020 cruk.org
SCIENTIFIC
REPORT
COVER IMAGE
Tissue microarray cores from triple-negative
breast cancer needle biopsies were subjected to
multiplex immunofluorescence. Nuclei are
2020
labelled in blue; cancer cells labelled in green
with a pan-cytokeratin antibody. CD45,
expressed by all immune cells, is in red, and
CD3, expressed only by T cells, is in yellow.
Image supplied by Christopher Bromley MANCHESTER
INSTITUTE
(Cancer Inflammation and Immunity)
CONTENTS
DIRECTOR’S INTRODUCTION 04 Tim Somervaille 32 RESEARCH SERVICES RESEARCH PUBLICATIONS 64
RESEARCH HIGHLIGHTS 2020 07 Leukaemia Biology Duncan Smith 52 SEMINAR SERIES 2020 72
Richard Marais 34 Biological Mass Spectrometry Facility
OPERATIONS 73
CANCER RESEARCH UK Molecular Oncology Jennifer Hughes and Joanna Roberts 53
MANCHESTER INSTITUTE Biological Resources Unit POSTGRADUATE EDUCATION 82
Esther Baena 36
Prostate Oncobiology Jeff Barry 54 THESES 86
RESEARCH GROUPS
Amaya Virós 38 Flow Cytometry CANCER RESEARCH UK’S LOCAL 88
Caroline Dive 16
Skin Cancer and Ageing Garry Ashton 55 ENGAGEMENT AND DEVELOPMENT
Cancer Biomarker Centre
Georges Lacaud 40 Histology ACKNOWLEDGEMENT FOR FUNDING OF 90
Santiago Zelenay 20 THE CANCER RESEARCH UK
Cancer Inflammation and Immunity Stem Cell Biology Wolfgang Breitwieser 57
MANCHESTER INSTITUTE
Claus Jørgensen 42 Molecular Biology Core and
Iain Hagan 22 CAREER OPPORTUNITIES AT THE CANCER 91
Systems Oncology Computational Biology Support Facility
Cell Division RESEARCH UK MANCHESTER INSTITUTE
Michela Garofalo 44 Marek Dynowski 58
Maximiliano Portal 24 CONTACT DETAILS 92
Transcriptional Networks in Lung Cancer Scientific Computing
Cell Plasticity & Epigenetics
Robert Bristow 46 Natalia Moncaut 60
Angeliki Malliri 26
Translational Oncogenomics Transgenic Production Facility
Cell Signalling
Patricia Muller 48 Steve Bagley 61
Caroline Springer 28
Tumour Suppressors Visualisation, Irradiation & Analysis
Drug Discovery
The Cancer Research UK Manchester Institute is temporarily located at Alderley Park in Cheshire until we return to our original site in The Oglesby Cancer Research Building.
Withington. Some research groups and staff remain in the Oglesby Cancer Research Building.
2 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE 3
although attendance at these meetings became Cancer Inflammation and Immunity group
DIRECTOR’S
easier as it meant no travel and lower costs, we published in the journal Immunity that
did have to learn how to get the most from the antagonistic inflammatory profiles can
new format. I am delighted that many of our anticipate immune-dependent progressive or
INTRODUCTION staff attended national and international
meetings during the pandemic and that despite
regressive tumour growth.
the challenges, they managed to present their Embracing human cell studies, the Cell Division
work and get the all-important feedback on group developed an approach to synchronise
their research from the international human cell populations by exploiting the
community. I was also delighted the CRUK MI CDK4/6i drugs approved for breast cancer. Their
was invited to showcase our research at the approach, published in Open Biology, arrests
prestigious Royal Society Summer Science cells at the restriction point but, importantly,
In 2020 we experienced unprecedented challenges caused by Exhibition, so congratulations to the team that without affecting DNA integrity. This means that
put in the hard work to win this accolade. it is now possible to study transcription, DNA
the global COVID-19 pandemic. Our priority is the wellbeing Although the exhibition was postponed, our replication, DNA repair and chromatin biology in
and safety of our staff, so early in March we convened tri-weekly Tumour Microenvironment exhibit will be synchronised cells, features that cannot be
presented at next year’s online Royal Society studied in double thymidine blocked cells (the
meetings of the Institute’s Emergency Response and Business Summer Science Exhibition. traditional approach) because they are obscured
Continuity Committee (ERBCC) to manage our response to the by the accumulation of DNA damage. This
Despite the challenges, I am pleased that we important contribution will likely be widely
emerging crisis. In common with other research institutes, we continued to make excellent progress in our adopted, and they are using the approach to
Professor
Richard Marais closed our laboratories in late-March to protect our staff and research. Our Drug Discovery Unit continues to refine our understanding of the G2/M control.
develop exciting inhibitors to explore the Along these lines, the Cell Signalling group
prevent the virus from spreading through the Institute and therapeutic potential and biology of lysyl published an exciting study in the Journal of Cell
Director of the Cancer Research
UK Manchester Institute through our community. oxidase in cancer, published in the Journal of Science, which revealed that the RAC guanine
Medicinal Chemistry, Cancer Research and nucleotide exchange factor (GEF) TIAM1 also
Organic Process Research. They have regulates centriole duplication. Centrosomes
Our laboratories were fully closed for 11 weeks, workers, using our specialist 3D printer to create developed exciting new cancer targets with are composed to two centrioles, and they
and we started reopening in early June, albeit over 200 plastic PPE headbands for hospitals CRUK MI colleagues Iain Hagan (cancer cell coordinate DNA segregation during cell division.
with limited access and social distancing rules in across the region and donating our PPE to them. cycle target) and Claus Jorgensen (tumour The group found that TIAM1 associates with
place. During the closure, a core team remained I am very grateful to all of our staff who helped stroma target), and new interactions with centrosomes, but when TIAM1 is depleted, PLK4
on site to protect our research-critical activities, to support the national effort, and I am proud of Caroline Dive on biomarkers and with Stephen levels at the centrosome increase, causing
ensure that we maintained rigorous animal the magnificent response CRUK MI made. Taylor on PARG. They also published very centriole overduplication and chromosome
welfare standards, saved our vital experimental Although we had to pause our own research, exciting preclinical and clinical data in Annals of lagging in anaphase, which is known to drive
materials, and maintained our critical our skills were used very effectively to fight the Oncology, showing that the orally available malignant progression. Curiously, PLK4
infrastructure. Let me therefore start by thanking virus. well-tolerated RAF+SRC inhibitor 3833 is regulation by TIAM1 is independent of its GEF
the ERBCC for its exceptional guidance and help effective in RAS-driven cancers. The Cancer activity but does require binding to the F-box
throughout the pandemic, and a huge thank Most of our remaining staff worked from home, Biomarker Centre published papers in Nature protein βTRCP, suggesting that TIAM1 promotes
you to our staff who remained on site during this so it was important that we kept connected and Cancer and the Journal of Thoracic Oncology PLK4 degradation through βTRCP and
very difficult time to protect our core functions. supported each other. We held weekly virtual that describe inter and intra-tumour independently of RAC1 activation.
You showed exceptional team spirit, updates to keep staff informed on progress, the heterogeneity in small cell lung cancer (SCLC),
commitment and dedication, together ensuring ever-changing situation, to share news and to highlighting the potential of their CDX approach, Continuing their studies on high-risk prostate
that our response to the crisis was effective and take questions. We formed an Education and now used worldwide, to advance SCLC cancer, the Translational Oncogenomics group
proportional. Engagement group to explore methods for research. Their T7 ctDNA pipeline now includes published several authoritative reviews that
motivating home-working staff, and this ctDNA methylation profiling and is being used highlight the challenges faced by prostate
At the beginning of the lockdown a COVID-19 resulted in several very successful new online to subtype SCLC patients, explore Cancers of patients and their treating clinicians (Nature
testing hub, the Lighthouse Laboratory, was training sessions. Our STAy Committee once Unknown Origin, and improve early detection Disease Primers, Nature, Nature Comms). Also
established at Alderley Park. We entered a again stepped up to the plate with new ideas for of non-small cell lung cancer. They also moving into the prostate, the Stem Cell Biology
working partnership with the Lighthouse to get boosting morale such as their Quarantine launched their CRUK UpSMART programme to group found that RUNX1 is highly expressed in a
this essential national facility up and running. Quizzes. We held a very successful virtual bring digital solutions to early clinical trials. On subpopulation of prostate proximal luminal cells
Several of our senior leaders joined the Christmas Party (I believe my “how to make a the biomarker theme, my own Molecular that are castration-resistant, self-sustained and
Lighthouse management team to help establish no-cheese cheesecake” video is still available). Oncology group reported signatures that do not generate other luminal cells. Their work,
the laboratories and its important workflows, We took our internal and external seminar series predict which patients will respond to immune published in eLife, identifies a cell type from the
and we loaned the new facility equipment, online to create opportunities for continued checkpoint blockade immunotherapy and onset of prostate development and provides
including the vital PCR machines. Over 30 of discussion of our research, and to learn from which could therefore be used to refine patient new insight into prostate biology.
our highly skilled staff and students volunteered each other and colleagues from around the care (published in Nature Communications). In
to work in the Lighthouse Laboratories and were world. I am grateful to all those who embraced Nature Cancer, we published that T cell The Leukaemia Biology group continued to
amongst the first to be trained to start testing these very successful seminar series, particularly evolution in response to immunotherapy can be co-develop the LSD1 inhibitor ORY-1001 (now
samples from front-line NHS workers, allowing our invited speakers who committed so much monitored using human blood samples, called iadademstat) reporting in the Journal of
those with negative tests to quickly return to of their time to the (initially) rather alien format of providing a tractable and convenient approach Clinical Oncology that the compound has a
patient care. Our staff members also found the virtual talk. International meetings also went to determine which patients are likely to good safety profile. The Tumour Suppressors
other innovative ways to support front line NHS online or, at best, adopted a hybrid format, so respond to these treatments. In this vein, the Group identified an intriguing role for copper in
4 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE DIRECTOR’S INTRODUCTION 5
DIRECTOR’S INTRODUCTION (CONTINUED)
regulation of p53 (published in Cell Death and with renewed vigour. It is testament to our core RESEARCH
Disease) and developed powerful tools for their
research (published in Cancer Cell
International). Finally, the Skin Cancer & Ageing
values and the strengths of the culture and
community that is CRUK MI. HIGHLIGHTS
group reported an intriguing sex bias in skin Finally, this is my last Annual Report, because
cancer, with men presenting more aggressive after 9 years I decided to step down as Director
disease (published in Clinical Cancer Research). to explore other opportunities. It is an exciting
Details of these discoveries and many more are time for the Institute. The Paterson Building has
in the specific reports from individual groups,
so please read on.
been demolished and, at extraordinary speed,
its replacement is emerging from the hole it left.
In this section we highlight some research publications from
Our move into this new facility is scheduled for 2020 which report significant advances in specific areas. The
Congratulations to all our staff who won prizes
and awards last year. The 2020 Dexter award
early 2023 and will provide opportunities to
build the Institute in new directions. I wish
selected papers demonstrate the breadth and the quality of the
was awarded to Wendy Trotter (Cell Division). Caroline Dive and Iain Hagan all the best as they research being undertaken by the groups at the Cancer
Bettina Wingelhofer (Leukaemia Biology) won a
John Goldman Fellowship from Leukaemia UK,
prepare for this important milestone in our
history. As I step away, let me reflect that while I
Research UK Manchester Institute.
and Sara Valpione (Molecular Oncology) won a am sad to move on, I am proud of the Institute I
Career Development Award from the Harry J have handed over. So let me end as I started, by Valpione S, Galvani E, Tweedy J, Mundra PA, some forms of immunotherapies, so the group
Lloyd Charitable Trust and was selected to thanking people. First, my thanks to CRUK and Banyard A, Middlehurst P, Barry J, Mills S, Salih called these cells T-immune effector or TIE cells.
participate in the ESMO Leaders Generation The University of Manchester for allowing me Z, Weightman J, Gupta A, Gremel G, Baenke F, Their studies contribute to improving our
Programme 2020. Santiago Zelenay (Group the privilege of leading CRUK MI; it was hard Dhomen N, Lorigan PC, Marais R. understanding of the mechanisms that mediate
Leader, Cancer Inflammation and Immunity) work, but it was also a lot of fun. My thanks to Immune awakening revealed by peripheral effective immune-responses to immune-
and I were awarded the inaugural BIAL Prize in Caroline Dive for your friendship, hard work and T cell dynamics after one cycle of checkpoint blockade drugs, so the data opens
Biomedicine together with other colleagues. guidance as Deputy Director; you contributed immunotherapy. new opportunities to design effective immune-
Alex de Feu (Prostate Oncobiology) won the so much to the growth of the Institute over the Nature Cancer 2020; 1(2):210-221. biomarkers for future clinical development. The
BioRad International Science writing last decade. Thank you to Caroline Wilkinson study also opens new avenues to further exploit
competition, Denys Holovanchuk (Molecular and Stuart Pepper for your friendship, In this publication, the Molecular Oncology the immune system for therapeutic gain.
Oncology) won an AACR Annual Meeting Travel unflinching dedication, and hard work; you group show that liquid biopsies can be used to Critically, because both parameters can be
Award, and Hannah Reed (Cell Signalling) won made my job easier, and you make the Institute identify which patients will benefit from measured using patient blood, responding
the prize for the best talk at the virtual Actin a fantastic place at which to do research. Thank immunotherapy. They demonstrate that patients can be identified early during treatment,
Meeting. Finally, Caroline Dive (Cancer you to Margaret Lowe and Mike Berne for following immunotherapy, T cell receptors with all of the advantages associated with
Biomarker Centre) won the Johann Anton managing our massively complex budgets and evolve to increase diversity or clonality in minimally invasive liquid biopsies. Early
Merck Award for Outstanding Preclinical to Rachel Powell for your assistance and patients who will go on to respond, but not in identification of responses will improve
Research in Oncology, was elected an EMBO guidance throughout. Thank you to the Group patients who do not respond. They also outcomes for patients, because it will allow
Member and became President of the Leaders and Core Facility Managers for guiding identify a subset of circulating T cells that therapies to be refined and personalised to the
European Association of Cancer Research. your units so productively. Thank you to my expand in patients who go on to respond, but individual. This will also reduce toxicity, because
own group for your productivity and the not in patients who do not respond. These cells non-responding patients can be spared
Despite working from home, our staff and impressive body of work we generated over the are characteristic of cells that fight infections, extended treatments that will not provide any
students continued to fundraise for CRUK. I last decade. Thank you to Ruth Cox, my but this data suggests that the same cells are benefit.
joined a Drug Discovery Unit Race for Life at Executive Assistant for your unwavering recruited to fight tumours in patients receiving
Home Challenge that raised over £3,000, and support, for steadying the ship when needed
Steve Lyons and the ‘Manchester Scientists’ and, with help from your assistants, for making
raised over £2,200 for the Stockport Relay for sure I was always prepared and in the right place
The Molecular Oncology group
Life. These are impressive achievements, so at the right time; without you it would have been
identified an immune signature of
thank you to everyone who took part and chaos. Finally, thank you to everyone who response to anti-PD1 drugs
everyone who sponsored us. worked at the Institute over the last decade; analysing peripheral blood T cells
your hard work and scientific contributions have and the T cell receptor DNA
We have faced adversity before and are still taken us closer to our aim of beating cancer sequences in cfDNA of cancer
patients receiving
recovering from the 2017 Paterson Building fire, sooner.
immunotherapy.
but challenge forces us to discover new and
sometimes better ways of pursuing our goals This artwork was designed for the
and working together. The pandemic has publication. (Image supplied by
reminded me that the Institute is its people and Sara Valpione, Molecular
Oncology)
that you are strong, resilient, and productive.
You continue to thrive, and I am delighted to
see the dedication of our staff, now back in the
laboratories. Thank you for toughing it out, for
sticking together and for pursuing your projects
6 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE RESEARCH HIGHLIGHTS 7
RESEARCH HIGHLIGHTS (CONTINUED) Salamero O, Montesinos P, Willekens C, pharmacokinetics, pharmacodynamics and
Pérez-Simón JA, Pigneux A, Récher C, Popat R, efficacy.
Carpio C, Molinero C, Mascaró C, Vila J, Arévalo
Galvani E, Mundra PA, Valpione S, Garcia- Pearsall SM, Humphrey S, Revill M, Morgan D, MI, Maes T, Buesa C, Bosch F, Somervaille TCP. Twenty-seven patients were treated with
Martinez P, Smith M, Greenall J, Thakur R, Frese KK, Galvin M, Kerr A, Carter M, Priest L, First-in-Human Phase I study of Iadademstat iadademstat on days 1 to 5 of each week in
Helmink B, Andrews MC, Boon L, Chester C, Blackhall F, Simpson KL, Dive C. (ORY-1001): A first-in-class lysine-specific 28-day cycles in a dose-escalation phase that
Gremel G, Hogan K, Mandal A, Zeng K, Banyard The rare YAP1 subtype of SCLC revisited in a histone demethylase 1a inhibitor, in relapsed or resulted in a recommended dose of 140 µg/m2/
A, Ashton G, Cook M, Lorigan P, Wargo JA, biobank of 39 circulating tumor cell patient refractory acute myeloid leukemia. day. This dose was chosen to treat all patients in
Dhomen N, Marais R. derived explant models: a brief report. Journal of Clinical Oncology 2020; 38(36):4260- an extension-cohort enriched with patients with
Stroma remodeling and reduced cell division Journal of Thoracic Oncology 2020; 4273. MLL-rearranged AML. Most adverse events were
define durable response to PD-1 blockade in 15(12):1836-1843. as expected and included myelosuppression
melanoma. Acute myeloid leukaemia is a haematological and non-hematologic events, such as
Nature Communications 2020; 11(1):853. Small cell lung cancer is an aggressive malignancy characterised by a block in myeloid infections, asthenia, mucositis, and diarrhoea.
neuroendocrine (NE) cancer with poor lineage differentiation. It remains, for the most Pharmacokinetic data demonstrated a dose-
Immune checkpoint inhibitors (ICIs) have prognosis, characterised by high circulating part, an incurable disease, especially in the dependent increase in plasma exposure, and
revolutionised the treatment of melanoma, tumour cell burden and early widespread elderly, and new approaches to treatment are pharmacodynamic data confirmed a potent
with checkpoint blocking antibodies to CTLA-4 metastasis. required, including those that promote time- and exposure-dependent induction of
and PD-1/PD-L1 improving survival for many differentiation. Certain epigenetic regulators are differentiation biomarkers. Reductions in blood
patients, and eliciting long-term durable Four consensus subtypes were proposed under evaluation as therapeutic targets, and bone marrow blast percentages were
responses for some. However, the biological recently for molecular classification of SCLC, including lysine-specific demethylase 1 (LSD1). observed, together with induction of blast cell
features underlying these durable responses defined by the expression of NE transcription LSD1 exhibits demethylase activity versus differentiation, in particular in patients with MLL
remain poorly understood. Efforts to identify factors ASCL1 and NEUROD1, the POU2F3 methylated lysine residues as well as a translocations. One complete remission with
markers of response in patient-derived secretory tuft cell lineage marker and YAP1, a transcription factor scaffolding activity. incomplete count recovery was observed in the
materials have been limited by the diversity and transcriptional activator with diverse roles dose escalation arm. Thus, iadademstat exhibits
plasticity of the immune system in a human culminating in pro-survival, pro-metastatic and Preclinical studies from the Leukaemia Biology a good safety profile together with signs of
population shaped by diverse variables such as chemoresistance oncogenic functions. SCLC group revealed that LSD1 sustains the clinical and biologic activity as a single agent in
genetic background, lifestyle and prior lines of cells predominantly express NE phenotypic differentiation block in certain molecular patients with AML.
treatment. In recent years, the Molecular markers, however it is known that a small subtypes of AML, in particular MLL-translocated
Oncology group reported that its BRAF V600E/ minority of these NE cells can transition to a AML. Iadademstat is a highly selective and
UVR-driven mouse melanoma model non-neuroendocrine (non-NE) phenotype, and potent covalent inhibitor of LSD1. Iadademstat Williams MS, Basma NJ, Amaral FMR, Williams
recapitulates the cardinal pathological and many of the Cancer Biomarker Centre’s was evaluated in a first-in-human dose- G, Weightman JP, Breitwieser W, Nelson L,
genomic features of human melanoma CTC-derived explant (CDX) models of SCLC also escalation and extension-cohort phase I study Taylor SS, Wiseman DH, Somervaille TCP.
including a UVR-induced mutational signature contain low numbers of non-NE cells, which in patients with refractory or relapsed acute Targeted nanopore sequencing for the
and high C-to-T mutation burden. Critically, are marked by expression of the NE repressor myeloid leukaemia. The primary objective was identification of ABCB1 promoter translocations
this model retains the mouse’s native immune protein, REST. Whilst the team were unable to to assess safety and tolerability of iadademstat; in cancer.
system and tumour microenvironment (TME), identify the YAP1 subtype in their global secondary objectives were to study BMC Cancer 2020; 20(1):1075.
while allowing control of genomic, behavioural transcriptomics analysis of 39 CDX models, they
and environmental variables. In this identified several models that had relatively high
publication, the Molecular Oncology group expression of YAP1 transcript. In the majority of
used this controlled system to assess the these models, YAP1 expression was co-localised
A549 cells invading into artificial
genetic and phenotypic changes induced by with REST, and thus restricted to localised
basement membrane following
PD-1 blockade and report that anti-PD-1 clusters of minority non-NE cell subpopulations. metal exposure.
treatment yielded responses in ~35% of A rare, ‘NE-low’ (i.e. expressing low levels of NE
tumours, and prolonged survival in ~27% of the markers by multiple metrics) SCLC phenotype Image supplied by Yannick
animals, similar to the responses observed in was also observed in their CDX biobank and in von Grabowiecki (Tumour
Suppressors)
the human patient population. From RNA these, YAP1 expression was more abundant and
sequencing, the group identified genes whose present both in NE and non-NE cells. When
expression correlated to response to PD-1 culturing the separated NE and non-NE cells
blockade, allowing the development of two from individual CDX models ex vivo, they found
signatures that were predictive of later that the non-NE, YAP1-expressing cells were
response, one for stroma remodelling and one more chemoresistant than their NE counterpart
for proliferation. Their signatures were validated cells. Together, these data indicate that YAP1
in two independent early on-treatment expression in SCLC represents an additional
anti-PD-1 patient cohorts. Together, these data feature of SCLC phenotypic heterogeneity, and
suggest that stroma remodelling and warrants further exploration in order to
proliferation are features of response to understand and exploit these differences for
immunotherapy that could be used to identify therapeutic gain.
responding patients so that treatment can be
tailored to achieve the best outcome for
individual patients.
8 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE RESEARCH HIGHLIGHTS 9
RESEARCH HIGHLIGHTS (CONTINUED) In non-small cell lung cancer (NSCLC), small retain their ability to resume synchronous cell
molecule inhibitors that target mutant kinases cycling. That time can be used to manipulate
have offered unprecedented success in the any molecule and when the cells are returned to
Resistance to chemotherapy is the most This approach proved an efficient method for management of the disease. One of the most the cycle, their fate can be observed and enable
common cause of treatment failure in acute identifying ABCB1 structural variants in THP-1 successful examples is echinoderm significant insights to be made into the function
myeloid leukaemia (AML) and the drug efflux AML cells and HGSC, identifying both novel and microtubule like-4-anaplastic lymphoma kinase of molecules and the behaviour of cells within
pump ABCB1 is a critical mediator. Recent previously described promoter translocations in (EML4-ALK)-mutant lung cancer, which affects the actual cycle under study.
studies have identified promoter translocations HGSC. In contrast, activating ABCB1 promoter 4-5% of lung cancer patients. EML4 causes the
as common drivers of high ABCB1 expression in translocations were not identified in ABCB1high constitutive activation of the The gold standard for cell cycle synchronisation
recurrent, chemotherapy-treated high-grade AML. H3K27Ac ChIP sequencing demonstrated ALK kinase domain which leads to cancer. To has long been the double thymidine block
serous ovarian cancer (HGSC) and breast significant activity of native promoters in all date, the first-generation ALK inhibitor crizotinib, approach, which stops the cell cycle at the
cancer. These fusions place ABCB1 under the cases of ABCB1high AML studied, consistent with second-generation ALK inhibitors ceritinib, phase of DNA replication and causes DNA
control of a strong promoter while leaving its endogenous regulation. alectinib and brigatinib, and the third- damage. The subsequent cell cycle is therefore
open reading frame intact. The mechanisms generation ALK inhibitor lorlatinib have been far from normal, making the double thymidine
controlling high ABCB1 expression in AML are Despite frequent high-level expression of ABCB1 approved by the Food and Drug Administration block approach difficult to study the
largely unknown. The Leukaemia Biology in relapsed primary AML, they found no (FDA) for the treatment of patients with lung biochemistry of DNA replication or
group therefore established an experimental evidence of ABCB1 translocations and instead cancer harbouring the EML4-ALK translocation. transcription, or chromatin biology. By contrast,
system and analysis pipeline to determine confirmed activity of native ABCB1 promoters. using CDK4/6 inhibitors clinically approved to
whether promoter translocations account for These findings are consistent with the group’s While initial responses are excellent, patients treat breast cancer have no impact upon DNA
high ABCB1 expression in cases of relapsed recent work describing the regulation of ABCB1 eventually relapse due to the development of integrity, making the Cell Division group’s
human AML. by a network of stress responsive enhancers in acquired resistance to these therapies. Exploring approach a game changer for researchers
primary AML. these mechanisms of resistance, the studying DNA biology. Critically, this publication
The group first demonstrated that prolonged Transcriptional Networks in Lung Cancer group shows that a drug developed to treat cancer,
in vitro daunorubicin exposure could induce found that EML4-ALK cells parental or resistant and with great effect, can now advance our
activating ABCB1 promoter translocations in a Paliouras AR, Buzzetti M, Shi L, Donaldson IJ, to crizotinib, ceritinib or alectinib are remarkably understanding of cell division to help identify
human AML cell line (THP-1), similar to those Magee P, Sahoo S, Leong HS, Fassan M, Carter sensitive to inhibition of genes involved in the further routes to cancer therapy.
recently described in recurrent high-grade M, Di Leva G, Krebs MG, Blackhall F, Lovly CM, cell cycle (namely, CDK7/12 with THZ1 and
serous ovarian and breast cancers. This model Garofalo M. CDK9) with drugs called alvocidib and dinaciclib.
was used to establish a targeted nanopore Vulnerability of drug-resistant EML4-ALK This treatment induces cell death through Bonavita E, Bromley CP, Jonsson G, Pelly VS,
long-read sequencing approach that was then rearranged lung cancer to transcriptional transcriptional inhibition and downregulation of Sahoo S, Walwyn-Brown K, Mensurado S,
applied to cases of ABCB1high HGSC and AML. inhibition. anti-apoptotic genes and reduces tumour Moeini A, Flanagan E, Bell CR, Chiang SC,
EMBO Molecular Medicine 2020; 12(7):e11099. growth not only in cancer cells but also in Chikkanna-Gowda CP, Rogers N, Silva-Santos
mouse models of the disease. In summary, B, Jaillon S, Mantovani A, Reis E Sousa C,
patients with acquired resistance to ALK Guerra N, Davis DM, Zelenay S.
inhibitors and wild-type ALK have only Antagonistic inflammatory phenotypes
Mutually exclusive expression of chemotherapy left as a treatment option. The dictate tumor fate and response to immune
the MYC family proteins MYC and
MYCL in CDX17P via multiplex
team’s findings point to the possibility that CDK checkpoint blockade.
immunofluorescence. MYC inhibition may be clinically tested as an Immunity 2020; 53(6):1215-1229.e8.
(green), MYCL (red), DAPI (blue), alternative to help manage this disease.
scale bar, 200 μm). Immunotherapy has emerged as an alternative
anti-cancer therapy, which has revolutionised
Image supplied by Kathryn
Simpson (Cancer Biomarker
Trotter EW, Hagan IM. the field of cancer research and treatment.
Centre) Release from cell cycle arrest with Cdk4/6 Unprecedented outcomes continue to be
inhibitors generates highly synchronized cell observed in multiple cancer types, including
cycle progression in human cell culture. malignancies where conventional therapies
Open Biology 2020; 10(10):200200. such as chemotherapy, radiotherapy or targeted
therapy have failed. Nevertheless, the
Iain Hagan and Wendy Trotter from the Cell immunotherapy excitement has been rapidly
Division group developed a new approach to tempered by clinical data showing that only a
synchronise the cell division cycle of an entire minority of cancer patients achieve complete
population of human cells in culture. This and long-lasting responses. This has
method, published in Open Biology, exploits the underscored the need for extensive preclinical
ability of CDK4/6 inhibitor drugs to arrest cell research to understand the basis of these
cycle progression at a natural pause point of the remarkable but still rare outcomes.
cycle: the restriction point. After synchronisation
and re-initiation of the cycle, all the cells in the Inflammation can fuel or inhibit cancer
population go through it at the same time and progression and the response to therapy. In this
rate, making it possible to perform biochemical study, the Cancer Inflammation and Immunity
and functional analyses of the changes that group investigated the signals and pathways that
occur in cells at specific points of the cycle. regulate the establishment of tumour
inflammatory microenvironments that support
Importantly, cells can be removed from the or restrain cancer progression. Combining the
cycle for up to 48 hours, during which they use of genetically engineered mouse cancer
10 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE RESEARCH HIGHLIGHTS 11
RESEARCH HIGHLIGHTS (CONTINUED) mechanisms by which they survive hormone
deprivation and subsequently regenerate the
prostate's complex cellular content, or are
involved in the emergence of castration-
The developing prostate of an resistant cells, remain to be elucidated. The
embryo with RUNX1 shown in
RUNX1 transcription factor is a master regulator
magenta.
of the blood system essential for hematopoietic
Image supplied by Renaud development, homeostasis, and disease.
Mével and Georges Lacaud Interestingly, there is increasing evidence
(Stem Cell Biology) implicating RUNX1 in the biology and pathology
of hormone-regulated tissues. Thus, the Stem
Cell Biology group systematically studied the
presence and contribution of RUNX1 expressing
cells during the development, homeostasis, and
regeneration of the prostate gland.
The group found that RUNX1 is highly expressed
in a subpopulation of proximal luminal cells
located at the base of the adult mouse prostate,
in the region next to the urethra. They
characterised these RUNX1+ luminal cells during
development and castration-regeneration
assays using single cells transcriptomics and
genetic lineage-tracing. They showed that
RUNX1+ luminal cells are castration-resistant,
self-sustained and do not regenerate other
distinct luminal cells types. They found that a
similar RUNX1+ population emerges in the
proximal region of the developing prostate
ducts during embryonic prostate development,
indicating that RUNX1+ proximal luminal cells are
an independent luminal cell type established at
the onset of prostate development. This Stem
models with the analysis of samples from Mevel R, Steiner I, Mason S, Galbraith LC, Patel Cell Biology study provides new insights into
cancer patients, the group identified Natural R, Fadlullah MZ, Ahmad I, Leung HY, Oliveira P, prostate development and the cellular
Killer (NK) cells as key drivers of cancer- Blyth K, Baena E, Lacaud G. composition of the mouse prostate epithelium.
inhibitory inflammation. In cancer models RUNX1 marks a luminal castration-resistant Investigating the functional relevance of these
rendered immunogenic by genetic ablation of lineage established at the onset of prostate RUNX1+ cells in prostate cancer, where the
the cyclooxygenase (COX)-2 pathway, NK cells development. presence of castration-resistant cells is a critical
were essential for initiating an inflammatory Elife 2020; 9:e60225. therapeutic problem, may open the door to
response that preceded and stimulated improved cancer treatments.
cytotoxic T cell-dependent tumour growth The prostate is a glandular organ of the
control. The analysis of patient datasets mammalian male reproductive system. A
suggested the COX-2 pathway regulates prostate luminal secretory epithelial
equally the cellular and molecular subpopulation is involved in fluid secretions that
inflammatory profile across multiple human form part of the semen. One incredible property
cancer types. Furthermore, the authors of the prostate epithelium is its plasticity. In the
developed an approach that by combining absence of hormones, such as chemical or
tumour-promoting and anti-tumour mediators surgical castration during prostate cancer
improves our ability to predict overall patient treatment, the prostate shrinks dramatically and
survival and the response to immunotherapy in loses most of the luminal cells. Strikingly, the
a wide range of human cancers. Collectively, prostate can fully regenerate itself upon
their findings established the COX-2 pathway hormone replenishment. This impressive
and NK cells as critical orchestrators of T regenerative capacity has been extensively
cell-mediated cancer immunity and demonstrated in mouse models, suggesting the
demonstrate the value of integrating pro- and presence of a subpopulation of cells with
anti-tumorigenic inflammation to predict specific regenerative properties. However, the
patient outcome. precise nature of these cells and the
12 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE RESEARCH HIGHLIGHTS 13
CANCER
RESEARCH UK
MANCHESTER
INSTITUTE
RESEARCH GROUPS
14 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE 15
www.cruk.manchester.ac.uk/Our-Research/Cancer-Biomarker-Centre Julie Stevenson
Jason Swift
Jenny Ward
Cancer Research UK Clinical Fellows
Manchester Institute Cancer
Alicia Conway
Victoria Foy
Melissa Frizziero
Biomarker Centre
Matthew Howell
Graduate Students
Oliver Bartley1
Alessia Catozzi
Jakub Chudziak
Victoria Gernedl 1
The goals of the CRUK Manchester Institute Cancer Biomarker Centre Sam Humphrey2
Alice Lallo2
(CBC) are a) to discover, develop, validate and implement biomarkers Julia Ogden
Sarah Pearsall
and digital solutions that optimise personalised cancer medicine; and Max Schenk
b) to characterise and exploit our panel of CDX models derived from Yitao Chen
circulating tumour cells from small cell lung cancer patient to discover Scientific Officers
new targets and test new therapies. Sophie Atkinson
Dominic Birch
Director Kieran Bradbury Figure 1.
Samuel Bratt 1 SCLC CDX non-NE cells form tubules with hollow lumens when cultured on Matrigel.
Caroline Dive CBC showcase studies published in Nature implicating a role for hypoxia-associated genes Stewart Brown A, Tubule formation of CDX17 non-NE cells visualised via brightfield (i) and fluorescence microscopy (ii). B,C, Confocal
Cancer and the Journal of Thoracic Oncology in VM and highlighting the plasticity of SCLC cells Debbie Burt Imaging of CDX17 non-NE cells forming hollow tubules visualised using Imaris software z-stack reconstruction, showing
Deputy Group Leader Holly Butterworth a defined outer tubule wall (Bi), with a hollow lumen (Bii, Biii) and cross sections of CDX17 non-NE cells showing a defined
Ged Brady2 that describe the inter- and intra-tumoural that can adapt and modulate their phenotypic
Mathew Carter cell containing an outer tubule wall (Ci), and continuous layer of cells forming the hollow centre (Cii and Ciii). All images
heterogeneity of SCLC, highlighting the potential characteristics to support tumour growth. We
Rebecca Carroll are representative.
Staff Scientists of the CDX approach, now used worldwide, to have also shown that formation of SCLC hollow Harry Clarke1
Alastair Kerr advance SCLC research. We submitted a patent tubular structures on matrigel (a VM surrogate Alex Clipson
Elaine Kilgour
presentation as a potential mechanism of relapse in early stage lung cancers and its
on our workflow for our T7 ctDNA pipeline that assay) occurs via active integrin signalling leading James Copley
Dominic Rothwell immune evasion. Generation of new CDX relationship with the broader immune landscape
incorporates ctDNA methylation profiling, and is to collagen deposition and remodelling (Figure Joanne Felce
Jonathan Tugwood Adam Freestone2
models with banking of matched PBMCs from of these tumours.
being deployed to subtype SCLC patients, 1). Our continued molecular characterisation of
Lynsey Franklin SCLC patients on immunotherapy is being
Associate Scientists explore Cancers of Unknown Origin, and for the VM seeks biomarkers and/or targets for non-NE
Melanie Galvin prioritised to enable CTC and T-cell co-culture We are also working with the digital ECMT team
Kris Frese early detection of non-small cell lung cancer. SCLC cell targeted therapies. Laura Glass studies. This co-culture capability is being and have demonstrated the feasibility of
Carlos Lopez-Garcia With clinical colleagues across the UK, Spain and Molly Glenister-Doyle extended to innate immune cell populations, detecting cytokines by ELISA in as little as 30μl
Kathryn Simpson Italy, we launched the CRUK Accelerator Biomarkers to inform immunotherapy trials Eleanor Gregory starting with natural killer cells. blood collected using a micro-sampler device,
UpSMART that will bring digital solutions to the The Cells and Proteins team (CAP) continue to Tatiana Guevara1
Service Manager As a first step towards testing of a COX- with optimisation of workflows for sample
care of patients undergoing early clinical trials. expand and develop the CBC immune Grace Hampson
Tony Price Michael Hoffs inflammatory signature as a predictive biomarker processing and analysis underway. This
biomarker ‘toolkit’. Through a new partnership
Elizabeth Hunter for immunotherapy in clinical trials, we are approach will be used in the NOTION study to
Postdoctoral Fellows Intra-tumoural functional heterogeneity with ThermoFisher, the IonTorrent platform is
Hayley Johnson working with Dr Santiago Zelenay (supported by evaluate home based blood sampling kits that
Katarzyna Bloch in SCLC now installed in our Tumour Immunology and Alex Jordan1 a MRC Confidence in Concept Award) to assess cytokines as an early warning system of
Francesca Chemi Using our CDX biobank, the Preclinical Inflammation Monitoring Laboratory and Noel Kelso
Ellyn Hughes
develop a standardised assay on the clinically adverse events and cytokine release syndrome in
Pharmacology team continue to explore and validation of TCRseq assays for analysis of Andrew McLeod1
Sumitra Mohan compatible NanoString platform to measure patients receiving immunotherapy and
describe novel elements of phenotypic diversity clonality, diversity and convergence in blood Simrah Mohammad
Maria Peiris-Pages expression of this signature in baseline patient advanced T-cell therapies. We are also working
within small cell lung cancer (SCLC) that were samples is ongoing. Working in close Derrick Morgan
Karen Morris tumour biopsies. A new ACED funded PhD with Dr Phil Monaghan, to enable transfer of our
Bioinformaticians not previously apparent due to the lack of collaboration with Prof Fiona Blackhall at the
Anthony Oojageer student is also working jointly between the cytokine and sTie2 ELISAs to the Christie Hospital
Phil Carter1 available tissue and patient-relevant models. The Christie Hospital Foundation Trust, the
Safwan Patel Zelanay group and CBC to explore the potential Diagnostic Biochemistry Laboratory for routine
Tine Descamps2 expanding panel of CDX models within our processing and banking of liquid biopsy samples Rosalind Pearson for the COX-inflammatory signature to predict NHS use and deployment in the upcoming
Saba Ferdous biobank (42 models, including 6 pairs) has from a cohort of SCLC patients receiving
Steven Hill 1 enabled us to build on our studies into acquired immunotherapy at the Christie is underway
Mukarram Hossain1 PBMCs / isolated
drug resistance, vasculogenic mimicry (VM) and allowing CTC, ctDNA and TCRseq analyses CDX / CTC immune cells
Cheryl Jones2
neurogenic transcription factor expression, aimed at identification of candidate biomarkers Figure 2. EDTA CTC isolation
Bedirhan Kilerci
particularly to understand the novel role of that predict and monitor patient responses to Circulating tumour cells (CTCs) blood
implantation /
Katarzyna Murat
ATOH1 in SCLC. immunotherapy. To complement these liquid and peripheral blood
Simon Pearce In vitro co-culture
mononuclear cells (PBMC) are CDX tumour
Matthew Roberts biopsies, T-cell infiltrates are being evaluated in
isolated from a patient blood
Cong Zhou Intra-tumour SCLC heterogeneity plays a role in SCLC tumour samples to develop an sample. CTCs can be cultured or Tumour reactive
Cytokine cocktail
metastasis and therapy resistance, with the understanding of the heterogeneity and implanted into mice to generate a Frozen T cell expansion
Clinical Informaticians Co-receptor antibodies
minority non-neuroendocrine (non-NE) cell mechanisms of immune evasion in advanced CTC Derived Explant Model (CDX) PBMC isolation Stored in liquid
Fouziah Butt
subpopulation supporting growth, survival and metastatic disease. Methods have also been in mice. CTCs or disaggregated nitrogen
Paul Fitzpatrick
dissemination of NE cells. We have shown that established for ex vivo co-cultures of peripheral CDX cells are co-cultured with
Hannah Frost
PBMC to determine the extent of
Andrew Hughes2 these non-NE cells are also the population that blood lymphocytes and disaggregated SCLC
tumour reactive T-cell activation.
Donal Landers are VM-competent, whereby an epithelial to CDX cells to enable investigation of anti-tumour Harvest tumour reactive T cells and
This system is being developed to
Leanne Ogden endothelial transition occurs to enable vessels T-cell responses and resistance to re-challenge against CTC / CDX cells
test the effect of therapeutics on
Paul O’Regan with blood transporting capabilities. RNA immunotherapy (Figure 2). A range of MHC1 the patient’s response to
Jenny Royle2
sequencing (RNAseq) of VM competent non-NE expression levels were observed across our immunotherapy.
Laura Stephenson
cells revealed a pseudo-hypoxic gene signature, SCLC CDX panel, highlighting impaired antigen Assess T cell IFN-γ production and
cytotoxic killing
16 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE CANCER BIOMARKER CENTRE 17CANCER BIOMARKER CENTRE (CONTINUED)
Jackie Pierce VALTIVE 1a trial (CI: Prof Gordon Jayson, cfDNA methylation pull-down assay that is
Alan Redfern University of Manchester/Christie NHS capable of high-throughput processing of the
Mitchell Revill
Foundation Trust - CFT) to optimise anti- large number of samples anticipated in early
Sophie Richardson1
Andrew Robb1
angiogenic therapy respectively. detection screens. The assay combines a
Caroline Roberts patented in-house NGS library preparation
Jordan Roebuck Nucleic acid-based biomarkers that direct method with a methyl-binding domain protein-
Karishma Satia therapy decisions based methylation enrichment approach. When
Daniel Slane-Tan The Nucleic Acids Biomarkers team has compared to other commercially available NGS
Karen Smith continued to develop and validate molecular library preparation kits, including those
Nigel Smith
profiling and disease monitoring liquid biopsy incorporating UMIs, our method had superior Bioinformatics and Biostatistics across the experiences electronically and remotely. The
Simon Topham
Hannah Walsh2
workflows to support clinical trials and performance in the cfDNA methylation assay, Cancer Biomarker Centre In-Home study, which assesses the feasibility of
Figure 3.
Daniel White translational projects across the CBC. resulting in increased enrichment and reduced (A) Improved enrichment and The Bioinformatics and Biostatistics (BBS) team is Acute Kidney Injury (AKI) detection in the patient’s
background (Figure 3A). We tested our on-target reads with CBC T7 active throughout the Cancer Biomarker Centre, home, was initiated with recent completion of
Junior Translational Scientist Mutational profiling of ctDNA to assist selection methylation assay on 20 NSCLC tumour samples approach. (B) Spike-in integrating bioinformatics and statistical methods Part A (with 12 Head and Neck cancer patients
Simon Hood of Phase I clinical trials (10 adenocarcinoma, 10 squamous cell experiments showed detection of
for its many and varied projects and providing enrolled). This trial measures renal function based
We profiled ctDNA in the TARGET Trial (Tumour carcinoma) and compared to published TCGA a cell line specific 300 region
Laboratory Manager DMR signature down to sensitivity input into experimental designs, including those on a pin-prick of blood and creatinine sensor.
chARacterisation to Guide Experimental data sets with good concordance seen between developed for the afore-mentioned NOTION trial The NOTION study (a CBC cross team project
Matthew Lancashire levels of 0.1-0.01% VAF (dotted
Targeted therapy, CI Matt Krebs UoM/CFT) with data sets confirming the accuracy of the CBC T7 blue line). (C) Using a 1022 DMR and the VALTIVE1a trial that seek to qualify our with the CAP team), has the objective of enabling
Laboratory Support Technicians completion of Part B (patient 520) expected by assay. We have also tested the sensitivity of the pan-cancer signature ctDNA liquid biopsy measuring sTie2 to instruct optimal dry blood spot technology to measure cytokine
Andrew Stevens the end of the year. Mutational analyses across assays in preliminary studies using 10 ng input methylation detected 49/51 use of anti-angiogenic therapy in ovarian cancer. levels in the home for early detection of immune-
Mahrukh Khurshid1 641 cancer-associated genes as well as copy spike-in experiments and shown the CBC T7 cancer patients (96% specificity)
A key focus is to enable robust, reproducible related toxicities, has been developed and will
number aberration (CNA) analysis were routinely assay is able to detect tumour specific across 4 tumour types.
CBC Programme Manager workflows to analyse different types of next- receive ethical approval in 2021.
presented at the monthly Molecular Tumour methylation signal at 0.01 - 0.1% VAF (Figure 3B). generation sequencing data. The TARGET trial
Ekram Aidaros-Talbot
Board. Analysis of immune biomarkers from Additional studies are currently on going to (CI: CBC alumnus, Matt Krebs) aims to match This year a digital ECMT Artificial Intelligence (AI)
COMPASS Study Project tumour biopsies to assist selection to further test the sensitivity and improve the patients with a broad range of advanced cancers capability was formally established within our
Manager immunotherapy trials was also added to the CBC bioinformatic analysis to enable calling of to early phase clinical trials; analysis of both team focussing on development of ethical AI and
Jonathan Wake TARGET biomarker portfolio over the past year tumour positive or negative samples. somatic mutations and copy number alterations investigation of novel algorithmic methods to
working alongside the CAP and Tissue across a 641 cancer-associated-gene panel in a deliver direct patient benefit. Aligned to this was
UpSMART Accelerator Project Biomarkers teams. We have used our methylation assay to generate
Manager single ctDNA assay support this aim. As TARGET development of the CORONET tool (COVID-19
a SCLC specific methylation signature derived is nearing completion, a final update on our data risk in Oncology Evaluation Tool) by digital ECMT
Akshita Patil 1
ctDNA analysis within the CACTUS and from tumour tissue and cfDNA from the same processing workflow will be used to rerun all the (with assistance from the BBS team) in
Administrative Coordinator DETECTION trials patient using a panel of 8 CDX tumours and the ctDNA analyses to provide a rich and internally collaboration with clinicians throughout the UK.
Suzanne Bickley Over the last year the NAB team has performed ctDNA isolated from the patient that gave rise to consistent dataset for exciting retrospective The decision support tool supports health care
GCP compliant droplet digital PCR (ddPCR) the CDX model. This comparison found a strong research. professionals in deciding which COVID-19
PA to the CBC Director analysis of ctDNA within the CACTUS Trial correlation between differentially methylated
Delydd Jones1
cancer patients to admit to hospital. A formal
(CirculAting Tumour DNA gUided therapy Switch, regions detected in both sample types, We are developing a custom pipeline and an R collaboration with University Hospital
CI Paul Lorigan UoM/CFT) for advanced confirming the viability of ctDNA as a source of software package for analysis of DNA CpG Southampton to deliver the REACT COVID-19
1
Joined in 2020
2
Left in 2020 cutaneous melanoma phase II patients. The methylation profiling. This signature is now being methylation to investigate chemoresistance in prospective observational study was also
ddPCR ctDNA assay measures mutated BRAF tested in a cohort of 99 SCLC cfDNA samples to patient derived mouse models, to determine established. As part of this, the REACT tool was
levels to instruct treatment switch from targeted determine the sensitivity and specificity of the SCLC subtypes and tissue-of-origin for Cancer of repurposed to enable hospital data to be
to immunotherapy and requires validated results SCLC classifier which will then be used to Unknown Primary (CUP) in cfDNA and within a visualised.
to be returned to the clinic within 7 days of blood monitor SCLC patients, identify early relapse and multi-modal liquid biopsy for early detection of
draw. Modification of the assay has enabled potentially give insight into mechanisms of lung cancer. The digital ECMT, along with our EU colleagues,
inclusion of more patients within the trial, with 23 resistance. including those from Fondazione IRCCS Istituto
patients screened to date. Validation of a more In a cross CBC team study with dECMT and with Nazionale dei Tumori Milano and Instituto de
extensive (11 targeted mutations) and sensitive The methylation workflow is also being used in a clinical colleagues across the UK (CI: Rebecca investigación Oncologica de Vall d’Hebron,
ddPCR-based primary clinical assay has also collaboration with Natalie Cook (UoM/CFT) on Lee, UoM/CFT), we assisted the development of a Barcelona was awarded a CRUK Accelerator
been developed within the group for use in the Cancer of Unknown Primary (CUP) study where machine learning platform to predict COVID Award, UpSMART, to enable SMART Experimental
DETECTION trial (Circulating tumour DNA tissue-specific methylation profiles will be used severity for cancer patients (see below). Cancer Medicine Trials. The 5-year UpSMART
guidEd Therapy for stage IIB/C BRAF or NRAS to identify the tissue of origin for these difficult to programme commenced in 2020 with the initial
mutant- positive mElanoma after surgiCal treat patients. To date we have applied the CBC Digital solutions to support treatment for aim of identifying digital healthcare products
resection, CI: Paul Lorigan). This trial involves T7 methylation approach to cfDNA analysis of cancer patients (DHPs) which are proving valuable to either/both
ddPCR ctDNA analysis to detect early relapse/ 37 HNVs and 51 cancer patient samples using The digital Experimental Cancer Medicines Team clinical trial data acquisition and data
micro-metastatic disease and select patients for a pan-cancer signature consisting of 1022 (digital ECMT) established several ‘technology’ interpretation from the network of (currently 24)
targeted therapy and will open to recruitment in differentially methylated regions (Figure 3C). clinical trials (software, algorithms, medical participating experimental cancer medicine
Q2 2021. NAB has now validated the lower levels This found that the pan-cancer signature could devices), which evaluate not only performance centres/early drug development units across
of detection for 4 BRAF mutations and 3 NRAS separate 49/51 cancer patient samples from characteristics of technology but also how they Europe. In year 1, the programme identified 29
mutations, with validation of 4 additional hTERT HNVs, even in samples where somatic mutation enable changes in the patient care pathway potential DHPs across the network and prioritised
mutations on going. analysis failed to detect a quantifiable VAF (lower inside and outside of hospitals. 10 of those to develop, using UpSMART
level of detection 1%). Further refinement of the Accelerator funding, into open-source accessible
Methylation profiling of ctDNA for the early methylation workflow and generation of more The PROACT Study was delivered, which products; free of license fees to use.
detection of cancers robust cancer specific methylation profiles are investigated the feasibility of implementing an
We have further refined our genome-wide currently on going. app for capturing patient reported outcomes and Publications listed on page 64
18 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE CANCER BIOMARKER CENTRE 19www.cruk.manchester.ac.uk/Our-Research/Cancer-Inflammation-and-Immunity Research Centre Biobank. Funded by a Medical
TME inflammatory profile Cancer Promoting
Ptgs2+/+ tumor PGE2 Research Council Confidence in Concept award
EP2 CP and in close collaboration with the Cancer
CANCER INFLAMMATION EP4
IFNγ
CI
IL-1
IL-6
CXCL1
...
Biomarker Centre and various oncologists and
pathologists from the NHS Christie Foundation
AND IMMUNITY
wild-type
Trust, we are developing a standardised protocol
Ptgs2-/- tumor
PGE2 to monitor the COX-IS in patient biopsies using a
CP
Cancer Inhibitory clinically-compatible platform. Using patient
IFNγ
samples from three tumour types, clear cell renal
wild-type
CI cancer, triple-negative breast cancer and
IL-12
Ptgs2+/+ tumor CXCL9 non-small cell lung cancer, we are evaluating the
PGE2 CXCL10 feasibility of an assay to accurately determine the
Immune checkpoint blockade therapy, especially that based on the IFNγ
CP ...
CTL-mediated
COX-IS in RNA extracted from formalin-fixed
eradication
use of PD(L)-1 targeted monoclonal antibodies, has transformed CI paraffin-embedded and validating its prognostic
EP2 & EP4-
cancer treatment becoming the standard of care for multiple deficient NK cells Tumor cells NK cells utility. We argue that establishing this protocol is a
Survival critical step to prospectively test the COX-IS
tumour types. Despite the advent of these transformative treatments, predictive power and to guide the selection of
few patients derive profound and long-lasting benefit. Moreover, our CP patients for immune checkpoint blockade
therapy alone or in combination with COX-2
ability to predict who will respond is very limited.
COX-IS CP
COX-IShigh inhibition. The latter combinations are currently
COX-ISlow
Group Leader CI being planned and evaluated across the globe
Santiago Zelenay Our group at the Cancer Research UK genetic ablation of the cyclooxygenase (COX)-2 CI including in Manchester in two clinical trials led
Manchester Institute investigates the signals and pathway, has uncovered antagonistic by Dr Anne Armstrong, a Consultant Medical
Postdoctoral Fellows αPD-(L)1 Oncologist from The Christie NHS Foundation
pathways that regulate the establishment of inflammatory profiles that anticipate immune- αCTLA-4
Eduardo Bonavita Trust. These trials will constitute ideal settings to
Agrin Moeini
tumour environments that favour anti-cancer dependent progressive or regressive tumour
immunity and response following growth (Bonavita et al, Immunity 2020; Figure 1). Pan-cancer analysis
Immunotherapy further examine the value of the COX-IS as
Victoria Pelly1 respose
immunotherapy. Under the central hypothesis relevant immune-biomarker.
Scientific Officer that the type of inflammatory response most Through deep cellular and molecular profiling of
Shih-Chieh Chiang prevalent in clinically-apparent tumours tumours formed by COX-2 competent or insensitive to prostaglandin E2 (PGE2) effects, the In direct connection with the translational and
promotes cancer progression, immune escape deficient cancer cells, we identified Natural Killer Figure 1. main factor that drives immune escape in our clinical implications of our findings in genetically-
Graduate Students modified cancer models, we have made
and therapy resistance, we combine the use of (NK) cells as central orchestrators of T cell- Graphical abstract of the study tumour models (Zelenay et al. Cell 2015),
Charlotte Bell significant progress in various other lines of
genetically engineered pre-clinical cancer mediated tumour immunity. While NK cells are published in Immunity by established NK cells as the main target of cancer
Christian Bromley
models with the analysis of patient samples to well known for their direct cytocidal activity Eduardo Bonavita et al.
cell-derived PGE2. investigation. This includes expanding our search
Eimear Flanagan
Searching for what makes for putative, common cancer cell-intrinsic
Maria Koufaki2 study the cellular and molecular inflammatory against cancer cells, in our experimental systems inflammation ‘good’ or ‘bad’, the
determinants that underpin immunotherapy we found that early accumulation of NK cell in Mining datasets from The Cancer Genome Atlas, immune evasive mechanisms or advancing our
Cancer Inflammation and
Clinical Fellow success. tumours is essential to drive an inflammatory we established that the pro-tumourigenic or understanding of the basis for the synergistic
Immunity group identified
Charles Earnshaw2
reprogramming characteristic of the so-called tumour cell-derived PGE2 anti-tumourigenic inflammatory landscapes effect of combining immunotherapy with COX-2
Since 2006, more than 3500 clinical trials have ‘hot’ T cell-inflamed tumours. Critically, while NK selectively acting on NK cells as a driven in murine models by PGE2 or NK cells, inhibitors. Likewise, we have further extended
1
Left in 2020 and deepened our examination of tumour
been started to test PD(L)-1 blockade as a cells themselves inhibited tumour growth, T major regulator of T cell- respectively, can also be found within human
2
Joined in 2020
monotherapy or in combination with other cells, and in particular cytotoxic T lymphocytes,
inflammation in murine models.
malignancies. Based on this observation, we human samples through bioinformatic analysis of
Based on these findings in murine large publicly available datasets. This analysis
agents. Many of these trials are still active and were indispensable for the full eradication of models, the team developed an
designed a gene-expression signature that, by
evaluate combination regimens of PD(L)-1 tumours. integrating cancer-promoting and inhibitory provided further compelling evidence for the
approach that improves our
antibodies with other immune checkpoint inflammatory mediators in one single indicator, intimate link between the ‘flavour’ of
ability to predict patient survival
inhibitor drugs (mainly anti-CTLA4 antibodies), The use of multiple genetically-modified mouse and response to immunotherapy exhibits powerful prognostic utility and predicts inflammation at the tumour bed and patient
chemotherapy, radiotherapy or targeted therapy. strains allowed us to ascribe IFN-γ as a critical in various cancer types. response to immunotherapy. This gene outcome and response to treatment.
Notwithstanding this central role of PD(L)-1 axis molecular mediator of NK cell activity. We signature, termed COX-IS (COX-inflammatory
blockade in clinical practice, our current showed that NK cell-derived IFN-γ drives an signature), is the subject of a patent application by All these studies have in turn opened new
understanding of the basis underlying therapy intratumoural inflammatory reprogramming that Cancer Research UK Commercial Partnerships research lines aimed at shedding light onto
response, resistance or relapse is limited. attracts and stimulates the differentiation of (http://commercial.cancerresearchuk.org/ questions such as ‘how other regularly used
Likewise, and very much connected to this anti-cancer effector T cells. Accordingly, single lo-biomarkers-search). The COX-IS showed value cancer treatments alter the inflammatory
central gap in knowledge, there is an urgent cell RNA sequencing analysis of tumour- for the prediction of responses and survival response at the tumour site’, or ‘how they
need to develop biomarkers to distinguish infiltrating immune cells revealed that the across multiple datasets from patients that influence other aspects of aggressive tumours,
responders from non-responders. Within this transcriptome of the most abundant leukocyte underwent immune checkpoint blockade, like recurrence or metastatic spread’. Equally, our
rapidly evolving clinical scenario, our group subsets in tumours, monocytes and tumour- independently of the cancer type or immune in-depth profiling of mice and human tumours
performs fundamental and translational associated macrophages, was enriched in checkpoint inhibitor drug used. Notably, the has identified candidate immune cell subsets
research to help answer these crucial open IFN-γ-driven signalling in NK cell competent COX-IS outperformed other current immune- with rather unique features. Despite being rare
questions in the immuno-oncology field. Our mice. In contrast, following the acute depletion biomarkers in anticipating outcome even in components of the whole leukocyte infiltrate, we
working hypothesis is that the inflammatory of NK cells, the transcriptional profile of tumour- cancer types in which tumour mutational burden speculate that their presence and/or activation
landscape at the tumour bed, before or shortly infiltrating myeloid cells showed a marked or PD-L1 expression do not, such as in clear cell status determine the magnitude and quality of
on-treatment, determines the outcome of enrichment in signalling pathways commonly renal cell carcinoma, the most common type of the local immune response. As such, we argue
immunotherapy. However, cancer-associated associated with malignant tumour growth. In kidney cancer. these poorly characterised cell-types define the
inflammation is a very complex process that agreement, tumours that spontaneously success of cancer treatments that rely on the
manifests in different ‘flavours’ with dual tumour- regressed in wild-type immunocompetent mice, Building on from these in silico analyses, we have cancer suppressing function of immunity.
promoting and restraining effects. Consistent grew progressively in mice lacking NK cells, or embarked on a research project aimed at
with this notion, our recent work in preclinical deficient in IFN-γ. Lastly, the use of genetically- developing a protocol to measure the COX-IS in Publications listed on page 65
cancer models rendered immunogenic by modified mice in which NK cells are selectively patient samples from the Manchester Cancer
20 SCIENTIFIC REPORT 2020 CANCER RESEARCH UK MANCHESTER INSTITUTE CANCER INFLAMMATION AND IMMUNITY 21You can also read
